diff --git a/tools/linuxfs/overlay/usr/local/bin/droiddeck-steam-compat b/tools/linuxfs/overlay/usr/local/bin/droiddeck-steam-compat
index 24b2ad88..e1ab89bf 100755
--- a/tools/linuxfs/overlay/usr/local/bin/droiddeck-steam-compat
+++ b/tools/linuxfs/overlay/usr/local/bin/droiddeck-steam-compat
@@ -442,27 +442,49 @@ class Helper:
             installed = COMPAT["installed_apps"](self.steam_root)
             self.installed = installed
             picks = COMPAT["valve_picks"](self.steam_root)
-            apps = sorted(set(installed) | set(picks) | set(state.get("auto", {})), key=COMPAT["app_order"])
+            prior_auto = state.get("auto", {})
+            if not isinstance(prior_auto, dict):
+                prior_auto = {}
+            prior_native = state.get("native", ())
+            native_choices = set(prior_native if isinstance(prior_native, (list, tuple, set)) else ())
+            apps = sorted(set(installed) | set(picks) | set(prior_auto) | native_choices, key=COMPAT["app_order"])
             overrides = COMPAT["requested_games"](
                 COMPAT["game_requests"](), catalog, [t["name"] for t in live])
             apps = sorted(set(apps) | set(overrides), key=COMPAT["app_order"])
             current = dict(page.compat("many(%s)" % json.dumps(apps)) or {})
             current["0"] = top["selected"]
-            native = COMPAT["native_targets"](self.steam_root, installed)
+            native = COMPAT["native_targets"](self.steam_root, apps)
+            raw_mapping = COMPAT["read_config_mapping"](
+                os.path.join(self.steam_root, "config", "config.vdf"))
+            if raw_mapping is None:
+                for app in native_choices:
+                    current[app] = ""
+            else:
+                for app in set(native) | native_choices:
+                    if app in raw_mapping:
+                        current[app] = raw_mapping[app]
+                    elif app in prior_auto or app in native_choices:
+                        current[app] = ""
             changes, auto = COMPAT["plan_mapping"](
                 current, installed, [t["name"] for t in live], default,
-                COMPAT["followers"](state, current), native, picks, overrides)
+                COMPAT["followers"](state, current), native, picks, overrides,
+                prior_auto.keys(), native_choices)
             for app, tool in sorted(changes.items(), key=lambda item: COMPAT["app_order"](item[0])):
-                page.compat("set(%d, %s)" % (int(app), json.dumps(tool)))
-                say("%s -> %s" % ("default" if app == "0" else "app %s" % app, tool))
-            state.update(auto=auto, tools=catalog, live=True)
+                page.compat("set(%d, %s)" % (int(app), json.dumps(tool if tool is not None else "")))
+                say("%s -> %s" % ("default" if app == "0" else "app %s" % app,
+                                   tool if tool is not None else "Steam native default"))
+            state.update(
+                auto={app: tool for app, tool in auto.items() if tool is not COMPAT["NATIVE_CHOICE"]},
+                native=sorted(app for app, tool in auto.items() if tool is COMPAT["NATIVE_CHOICE"]),
+                tools=catalog, live=True)
             if waiting:
                 state["pending"] = wanted
                 say("%s is new to the running client; it applies when Steam next starts" % wanted)
             else:
                 state.pop("pending", None)
             COMPAT["write_json"](state_file, state)
-        if native or os.path.exists(COMPAT["fex_wanted_marker"]()):
+        if (any(app in installed and tool == COMPAT["FEX_TOOL"] for app, tool in native.items()) or
+                os.path.exists(COMPAT["fex_wanted_marker"]())):
             for app in COMPAT["request_fex"](self.steam_root, self.fex_asked):
                 say("asked the client to install %s for x86 Linux titles and programs" % app)
 
diff --git a/tools/linuxfs/overlay/usr/local/bin/steam-compatibility b/tools/linuxfs/overlay/usr/local/bin/steam-compatibility
index 71557cf0..39149751 100755
--- a/tools/linuxfs/overlay/usr/local/bin/steam-compatibility
+++ b/tools/linuxfs/overlay/usr/local/bin/steam-compatibility
@@ -787,19 +787,18 @@ def native_targets(steam_root, apps):
         return {}
     targets = {}
     for app, (oslist, osarch, kind) in appinfo_platforms(os.path.join(steam_root, "appcache", "appinfo.vdf"), wanted).items():
-        if kind not in PLAYABLE_TYPES or "windows" in oslist or "linux" not in oslist:
+        if kind not in PLAYABLE_TYPES or "linux" not in oslist:
             continue
         if "arm64" in osarch or "aarch64" in osarch:
+            targets[app] = None
+            continue
+        if "windows" in oslist:
+            targets[app] = NATIVE_CHOICE
             continue
         targets[app] = FEX_TOOL
     return targets
 
 
-def linux_runtime_tool(name):
-    low = name.lower()
-    return low == "fex" or low.startswith("steamlinuxruntime")
-
-
 def fex_missing(steam_root):
     missing = []
     for app in FEX_DEPENDENCIES:
@@ -877,18 +876,22 @@ def app_order(app):
 
 
 DEFERRED_GAME_TOOL = object()
+NATIVE_CHOICE = object()
 
 
-def plan_mapping(current, installed, runnable, default, auto, native=None, picks=(), overrides=None):
+def plan_mapping(current, installed, runnable, default, auto, native=None, picks=(), overrides=None, managed=None,
+                 native_choices=()):
     runnable = {n.lower() for n in runnable}
     installed = set(installed)
     picks = set(picks)
     native = native or {}
     overrides = overrides or {}
+    managed = set(auto) if managed is None else set(managed)
+    native_choices = set(native_choices)
     changes, kept = {}, {}
     if current.get("0", "") != default:
         changes["0"] = default
-    for app in sorted((set(current) | installed | picks | set(auto) | set(overrides)) - {"0"}, key=app_order):
+    for app in sorted((set(current) | installed | picks | set(auto) | set(overrides) | native_choices) - {"0"}, key=app_order):
         name = current.get(app, "")
         if app in overrides:
             target = overrides[app]
@@ -902,9 +905,26 @@ def plan_mapping(current, installed, runnable, default, auto, native=None, picks
             continue
         mine = auto.get(app)
         target = native.get(app, default)
-        stale = unrunnable(name, runnable) or (app in native and linux_runtime_tool(name))
+        if not name and app in native_choices:
+            target = NATIVE_CHOICE
+        stale = unrunnable(name, runnable)
         if name and not stale and (mine is None or name != mine):
             continue
+        if target is NATIVE_CHOICE:
+            if not name and (app in native_choices or app in current or app in managed):
+                kept[app] = NATIVE_CHOICE
+                continue
+            target = default
+        if target is None:
+            if stale:
+                target = default
+                if name != target:
+                    changes[app] = target
+                continue
+            else:
+                if name and app in managed and name == mine:
+                    changes[app] = None
+                continue
         if not name and app not in installed and app not in picks:
             continue
         if name != target:
@@ -1043,8 +1063,37 @@ def read_mapping(tokens, mapping):
     return current
 
 
+def read_config_mapping(config_path):
+    """Read per-app choices without creating or rewriting the client's mapping block."""
+    try:
+        with open(config_path, encoding="utf-8", errors="replace") as f:
+            tokens = tokenize(f.read())
+    except OSError:
+        return None
+    depth = 0
+    for token in tokens:
+        if token == "{":
+            depth += 1
+        elif token == "}":
+            depth -= 1
+            if depth < 0:
+                return None
+    if depth != 0:
+        return None
+    steam = find_block(tokens, ["InstallConfigStore", "Software", "Valve", "Steam"])
+    if steam is None:
+        return None
+    mapping = find_block(tokens[steam + 1:], ["CompatToolMapping"])
+    return read_mapping(tokens, mapping + steam + 1) if mapping is not None else {}
+
+
 def set_mapping(tokens, mapping, app, tool):
     block = find_block(tokens[mapping + 1:], [app])
+    if tool is None:
+        if block is not None:
+            block += mapping + 1
+            del tokens[block - 1:block_end(tokens, block) + 1]
+        return
     if block is None:
         tokens[mapping + 1:mapping + 1] = [
             '"%s"' % app, "{", '"name"', '"%s"' % tool, '"config"', '""', '"priority"', '"75"' if app == "0" else '"250"', "}"]
@@ -1109,13 +1158,17 @@ def register_default(config_path, apps=(), protect=(), default=None, catalog=Non
         steam_root = os.path.dirname(os.path.dirname(os.path.abspath(config_path)))
         overrides = requested_games(game_requests(directory), catalog)
         changes, auto = plan_mapping(
-            current, apps, names, default, followers(state, current), native_targets(steam_root, apps), picks, overrides)
+            current, apps, names, default, followers(state, current),
+            native_targets(steam_root, set(apps) | set(picks)), picks,
+            overrides, state.get("auto", {}).keys() if isinstance(state.get("auto"), dict) else (),
+            state.get("native", ()))
         for app, tool in changes.items():
             set_mapping(tokens, mapping, app, tool)
         text = serialize(tokens)
         if text != serialize(tokenize(original)):
             write_changed(config_path, text)
-        state["auto"] = auto
+        state["auto"] = {app: tool for app, tool in auto.items() if tool is not NATIVE_CHOICE}
+        state["native"] = sorted(app for app, tool in auto.items() if tool is NATIVE_CHOICE)
         state["tools"] = catalog
         state.setdefault("default", default)
         write_json(state_path("state.json", directory), state)
diff --git a/tools/tests/test_droiddeck_fex.py b/tools/tests/test_droiddeck_fex.py
index 20ccad02..8142e1ab 100644
--- a/tools/tests/test_droiddeck_fex.py
+++ b/tools/tests/test_droiddeck_fex.py
@@ -499,19 +499,23 @@ class AppInfoTest(unittest.TestCase):
         table = struct.pack("<I", len(strings)) + b"".join(s.encode() + b"\0" for s in strings)
         return struct.pack("<IIq", magic, 1, table_at) + body + table
 
-    def test_linux_only_titles_are_sent_to_fex(self):
+    def test_linux_only_titles_are_sent_to_fex_and_dual_platform_is_deferred(self):
         for magic in (0x07564427, 0x07564428, 0x07564429):
             with tempfile.TemporaryDirectory() as tmp:
                 steam = Path(tmp)
                 (steam / "appcache").mkdir()
                 (steam / "appcache/appinfo.vdf").write_bytes(self.appinfo({
                     10: ("windows", "", "Game"), 20: ("linux", "64", "Game"), 30: ("windows,linux,macos", "", "game"),
-                    40: ("linux", "arm64", "game"), 50: ("linux", "", "Demo"), 70: ("linux", "", "Tool"), 80: ("linux", "", "config"),
+                    40: ("linux", "arm64", "game"), 41: ("windows,linux", "aarch64", "game"),
+                    50: ("linux", "", "Demo"), 70: ("linux", "", "Tool"), 80: ("linux", "", "config"),
                     90: ("linux", "", ""),
                 }, magic))
                 self.COMPAT["APPINFO_CACHE"].clear()
-                targets = self.COMPAT["native_targets"](str(steam), ["10", "20", "30", "40", "50", "70", "80", "90", "1628350", "60"])
-                self.assertEqual(targets, {"20": "droiddeck-fex", "50": "droiddeck-fex"}, hex(magic))
+                targets = self.COMPAT["native_targets"](str(steam), ["10", "20", "30", "40", "41", "50", "70", "80", "90", "1628350", "60"])
+                self.assertEqual(targets, {
+                    "20": "droiddeck-fex", "30": self.COMPAT["NATIVE_CHOICE"],
+                    "40": None, "41": None, "50": "droiddeck-fex",
+                }, hex(magic))
 
     def test_titles_with_a_valve_pick_are_found_installed_or_not(self):
         def deck(oslist, runtime, kind="game"):
@@ -545,14 +549,34 @@ class AppInfoTest(unittest.TestCase):
         self.assertEqual(changes, {"30": "GE-Proton11-7", "32": "GE-Proton11-7"})
         self.assertEqual(auto, {"30": "GE-Proton11-7", "32": "GE-Proton11-7"})
 
-    def test_the_mapping_sends_native_titles_to_fex_and_keeps_picks(self):
+    def test_automatic_native_mapping_uses_fex_and_keeps_explicit_tools(self):
         tool, fex = self.COMPAT["TOOL"], self.COMPAT["FEX_TOOL"]
         changes, auto = self.COMPAT["plan_mapping"](
             {"0": tool, "20": "fex", "21": "steamlinuxruntime_sniper", "22": "GE-Proton11-7"},
             ["20", "21", "22", "23", "24"], [tool, "GE-Proton11-7"], tool, {},
             {"20": fex, "21": fex, "22": fex, "23": fex})
-        self.assertEqual(changes, {"20": fex, "21": fex, "23": fex, "24": tool})
-        self.assertEqual(auto, {"20": fex, "21": fex, "23": fex, "24": tool})
+        self.assertEqual(changes, {"23": fex, "24": tool})
+        self.assertEqual(auto, {"23": fex, "24": tool})
+
+    def test_explicit_linux_runtime_and_fex_selections_survive_default_maintenance(self):
+        tool, fex = self.COMPAT["TOOL"], self.COMPAT["FEX_TOOL"]
+        changes, auto = self.COMPAT["plan_mapping"](
+            {"0": tool, "20": "steamlinuxruntime_arm64", "21": fex},
+            ["20", "21"], [tool], tool, {}, {"20": None, "21": fex}, ["20", "21"])
+        self.assertEqual(changes, {})
+        self.assertEqual(auto, {})
+
+    def test_native_arm64_default_stays_unmapped_and_old_auto_proton_is_cleared(self):
+        tool = self.COMPAT["TOOL"]
+        changes, auto = self.COMPAT["plan_mapping"](
+            {"0": tool, "20": tool}, ["20"], [tool], tool, {"20": tool}, {"20": None}, ["20"])
+        self.assertEqual(changes, {"20": None})
+        self.assertEqual(auto, {})
+
+        changes, auto = self.COMPAT["plan_mapping"](
+            {"0": tool}, ["20"], [tool], tool, {}, {"20": None}, ["20"])
+        self.assertEqual(changes, {})
+        self.assertEqual(auto, {})
 
     def test_the_tool_files(self):
         with tempfile.TemporaryDirectory() as tmp:
diff --git a/tools/tests/test_game_environment.py b/tools/tests/test_game_environment.py
index 06e06333..c8895457 100644
--- a/tools/tests/test_game_environment.py
+++ b/tools/tests/test_game_environment.py
@@ -26,6 +26,22 @@ def config_text(entries):
     return '"InstallConfigStore" { "Software" { "Valve" { "Steam" { "CompatToolMapping" { %s } } } } }' % mapping
 
 
+class ReadConfigMappingTest(unittest.TestCase):
+    def test_missing_parent_or_unbalanced_vdf_is_not_treated_as_absent_choices(self):
+        with tempfile.TemporaryDirectory() as tmp:
+            config = Path(tmp) / "config.vdf"
+            config.write_text('"InstallConfigStore" { "Software" { "Other" {} } }')
+            self.assertIsNone(COMPAT["read_config_mapping"](str(config)))
+            config.write_text('"InstallConfigStore" { "Software" { "Valve" { "Steam" {} }')
+            self.assertIsNone(COMPAT["read_config_mapping"](str(config)))
+
+    def test_valid_steam_parent_without_compat_mapping_has_no_per_app_choices(self):
+        with tempfile.TemporaryDirectory() as tmp:
+            config = Path(tmp) / "config.vdf"
+            config.write_text('"InstallConfigStore" { "Software" { "Valve" { "Steam" {} } } }')
+            self.assertEqual(COMPAT["read_config_mapping"](str(config)), {})
+
+
 class GameEnvironmentTest(unittest.TestCase):
     def test_the_install_script_evaluator_gets_its_scripts_marked_first(self):
         with tempfile.TemporaryDirectory() as tmp:
@@ -415,6 +431,218 @@ class ProtonDefaultTest(unittest.TestCase):
         self.assertEqual(changes, {"0": "GE-Proton11-7", "10": "GE-Proton11-7", "11": "GE-Proton11-7", "14": "GE-Proton11-7"})
         self.assertEqual(auto, {"10": "GE-Proton11-7", "11": "GE-Proton11-7", "14": "GE-Proton11-7"})
 
+    def test_windows_only_titles_still_follow_the_default(self):
+        changes, auto = COMPAT["plan_mapping"](
+            {"0": self.TOOL}, ["42"], self.NAMES, self.TOOL, {})
+        self.assertEqual(changes, {"42": self.TOOL})
+        self.assertEqual(auto, {"42": self.TOOL})
+
+    def test_native_arm64_default_clears_only_our_auto_mapping(self):
+        with tempfile.TemporaryDirectory() as tmp:
+            config = Path(tmp) / "config.vdf"
+            config.write_text(config_text([("0", self.TOOL), ("42", self.TOOL)]))
+            (Path(tmp) / "state.json").write_text(json.dumps({
+                "default": self.TOOL,
+                "auto": {"42": self.TOOL},
+            }))
+            globals_ = COMPAT["register_default"].__globals__
+            original_native_targets = globals_["native_targets"]
+            globals_["native_targets"] = lambda _root, _apps: {"42": None}
+            try:
+                COMPAT["register_default"](
+                    str(config), ["42"], catalog=self.CATALOG, directory=tmp)
+                first = config.read_bytes()
+                self.assertEqual(mapping_of(first.decode()), {"0": self.TOOL})
+                self.assertEqual(COMPAT["tokenize"](first.decode()),
+                                 COMPAT["tokenize"](config_text([("0", self.TOOL)])))
+                self.assertEqual(json.loads((Path(tmp) / "state.json").read_text())["auto"], {})
+
+                COMPAT["register_default"](
+                    str(config), ["42"], catalog=self.CATALOG, directory=tmp)
+                self.assertEqual(config.read_bytes(), first)
+            finally:
+                globals_["native_targets"] = original_native_targets
+
+    def test_saved_native_choice_survives_valve_pick_without_appinfo(self):
+        app = "452280"
+        with tempfile.TemporaryDirectory() as tmp:
+            root = Path(tmp)
+            steam = root / "Steam"
+            config = steam / "config/config.vdf"
+            config.parent.mkdir(parents=True)
+            (steam / "steamapps").mkdir()
+            (steam / "steamapps" / ("appmanifest_%s.acf" % app)).write_text("")
+            config.write_text(config_text([("0", self.TOOL)]))
+            (root / "state.json").write_text(json.dumps({
+                "default": self.TOOL,
+                "auto": {},
+                "native": [app],
+            }))
+
+            globals_ = COMPAT["register_default"].__globals__
+            original_native_targets = globals_["native_targets"]
+            globals_["native_targets"] = lambda _root, _apps: {}
+            try:
+                COMPAT["register_default"](
+                    str(config), [], catalog=self.CATALOG, directory=tmp, picks=[app])
+                self.assertEqual(mapping_of(config.read_text()), {"0": self.TOOL})
+                state = json.loads((root / "state.json").read_text())
+                self.assertEqual(state["auto"], {})
+                self.assertEqual(state["native"], [app])
+            finally:
+                globals_["native_targets"] = original_native_targets
+
+    def test_shortcuts_scanner_keeps_native_choice_for_unrelated_app_list(self):
+        app, added_shortcut = "452280", "3537741571"
+        with tempfile.TemporaryDirectory() as tmp:
+            root = Path(tmp)
+            steam = root / "Steam"
+            config = steam / "config/config.vdf"
+            config.parent.mkdir(parents=True)
+            (steam / "steamapps").mkdir()
+            (steam / "steamapps" / ("appmanifest_%s.acf" % app)).write_text("")
+            config.write_text(config_text([("0", self.TOOL)]))
+            (root / "state.json").write_text(json.dumps({
+                "default": self.TOOL,
+                "auto": {},
+                "native": [app],
+            }))
+
+            globals_ = COMPAT["register_default"].__globals__
+            original_native_targets = globals_["native_targets"]
+            globals_["native_targets"] = lambda _root, wanted: {
+                app: COMPAT["NATIVE_CHOICE"]
+            } if app in wanted else {}
+            try:
+                COMPAT["register_default"](
+                    str(config), [app], catalog=self.CATALOG, directory=tmp)
+                self.assertEqual(json.loads((root / "state.json").read_text())["native"], [app])
+
+                COMPAT["register_default"](
+                    str(config), [added_shortcut], catalog=self.CATALOG, directory=tmp)
+                state = json.loads((root / "state.json").read_text())
+                self.assertEqual(state["native"], [app])
+                self.assertEqual(state["auto"], {added_shortcut: self.TOOL})
+                self.assertEqual(mapping_of(config.read_text()), {
+                    "0": self.TOOL,
+                    added_shortcut: self.TOOL,
+                })
+            finally:
+                globals_["native_targets"] = original_native_targets
+
+    def test_factorio_preserves_an_observed_native_choice_despite_ambiguous_metadata(self):
+        with tempfile.TemporaryDirectory() as tmp:
+            steam = Path(tmp) / "Steam"
+            config = steam / "config/config.vdf"
+            config.parent.mkdir(parents=True)
+            config.write_text(config_text([("0", self.TOOL)]))
+            state = {"default": self.TOOL, "auto": {}}
+            (Path(tmp) / "state.json").write_text(json.dumps(state))
+
+            globals_ = COMPAT["native_targets"].__globals__
+            original_platforms = globals_["appinfo_platforms"]
+            globals_["appinfo_platforms"] = lambda _path, wanted: {
+                "427520": ({"linux", "macos", "windows"}, "", "game")
+            } if "427520" in wanted else {}
+            try:
+                native = COMPAT["native_targets"](str(steam), ["427520"])
+                self.assertIs(native["427520"], COMPAT["NATIVE_CHOICE"])
+
+                changes, auto = COMPAT["plan_mapping"](
+                    {"0": self.TOOL}, ["427520"], self.NAMES, self.TOOL, {}, native)
+                self.assertEqual(changes, {"427520": self.TOOL})
+                self.assertEqual(auto, {"427520": self.TOOL})
+
+                COMPAT["register_default"](
+                    str(config), ["427520"], catalog=self.CATALOG, directory=tmp)
+                self.assertEqual(mapping_of(config.read_text()), {"0": self.TOOL, "427520": self.TOOL})
+
+                state["auto"] = {"427520": self.TOOL}
+                (Path(tmp) / "state.json").write_text(json.dumps(state))
+                config.write_text(config_text([("0", self.TOOL)]))
+                COMPAT["register_default"](
+                    str(config), ["427520"], catalog=self.CATALOG, directory=tmp)
+                first = config.read_bytes()
+                self.assertEqual(mapping_of(first.decode()), {"0": self.TOOL})
+                self.assertEqual(COMPAT["tokenize"](first.decode()),
+                                 COMPAT["tokenize"](config_text([("0", self.TOOL)])))
+                self.assertEqual(json.loads((Path(tmp) / "state.json").read_text())["auto"], {})
+                self.assertEqual(json.loads((Path(tmp) / "state.json").read_text())["native"], ["427520"])
+
+                COMPAT["register_default"](
+                    str(config), ["427520"], catalog=self.CATALOG, directory=tmp)
+                self.assertEqual(config.read_bytes(), first)
+
+                config.write_text(config_text([("0", self.TOOL), ("427520", "")]))
+                COMPAT["register_default"](
+                    str(config), ["427520"], catalog=self.CATALOG, directory=tmp)
+                native_choice = config.read_bytes()
+                self.assertEqual(mapping_of(native_choice.decode()), {"0": self.TOOL, "427520": ""})
+                self.assertEqual(json.loads((Path(tmp) / "state.json").read_text())["auto"], {})
+                self.assertEqual(json.loads((Path(tmp) / "state.json").read_text())["native"], ["427520"])
+                COMPAT["register_default"](
+                    str(config), ["427520"], catalog=self.CATALOG, directory=tmp)
+                self.assertEqual(config.read_bytes(), native_choice)
+
+                for choice in (COMPAT["FEX_TOOL"], COMPAT["TOOL_11"], "GE-Proton11-7"):
+                    config.write_text(config_text([("0", self.TOOL), ("427520", choice)]))
+                    COMPAT["register_default"](
+                        str(config), ["427520"], catalog=self.CATALOG, directory=tmp)
+                    self.assertEqual(mapping_of(config.read_text()), {"0": self.TOOL, "427520": choice})
+                    self.assertEqual(json.loads((Path(tmp) / "state.json").read_text())["native"], [])
+
+                state = json.loads((Path(tmp) / "state.json").read_text())
+                state["native"] = ["427520"]
+                state["auto"] = {}
+                (Path(tmp) / "state.json").write_text(json.dumps(state))
+                config.write_text(config_text([("0", self.TOOL), ("427520", "proton_experimental")]))
+                COMPAT["register_default"](
+                    str(config), ["427520"], catalog=self.CATALOG, directory=tmp)
+                self.assertEqual(mapping_of(config.read_text()), {"0": self.TOOL, "427520": self.TOOL})
+                saved = json.loads((Path(tmp) / "state.json").read_text())
+                self.assertEqual(saved["native"], [])
+                self.assertEqual(saved["auto"], {"427520": self.TOOL})
+            finally:
+                globals_["appinfo_platforms"] = original_platforms
+
+    def test_native_arm64_preserves_a_proton_mapping_without_managed_state(self):
+        changes, auto = COMPAT["plan_mapping"](
+            {"0": self.TOOL, "42": self.TOOL}, ["42"], self.NAMES, self.TOOL,
+            {"42": self.TOOL}, {"42": None}, managed=())
+        self.assertEqual(changes, {})
+        self.assertEqual(auto, {})
+
+    def test_native_arm64_keeps_a_chosen_valve_proton_through_its_wrapper(self):
+        changes, auto = COMPAT["plan_mapping"](
+            {"0": self.TOOL, "42": "proton_experimental"}, ["42"], self.NAMES,
+            self.TOOL, {}, {"42": None})
+        self.assertEqual(changes, {"42": self.TOOL})
+        self.assertEqual(auto, {})
+
+        changes, auto = COMPAT["plan_mapping"](
+            {"0": self.TOOL, "42": self.TOOL}, ["42"], self.NAMES,
+            self.TOOL, {}, {"42": None})
+        self.assertEqual(changes, {})
+        self.assertEqual(auto, {})
+
+    def test_native_arm64_keeps_explicit_runtime_fex_and_proton_profiles(self):
+        fex = COMPAT["FEX_TOOL"]
+        current = {
+            "0": self.TOOL,
+            "42": COMPAT["TOOL_11"],
+            "43": "GE-Proton11-7",
+            "44": "steamlinuxruntime_arm64",
+            "45": fex,
+            "46": "",
+        }
+        changes, auto = COMPAT["plan_mapping"](
+            current, ["42", "43", "44", "45", "46"], self.NAMES, self.TOOL, {},
+            {app: None for app in ("42", "43", "44", "45", "46")},
+            overrides={"46": "GE-Proton11-7"},
+        )
+        self.assertEqual(changes, {"46": "GE-Proton11-7"})
+        self.assertEqual(auto, {})
+
     def test_titles_following_the_default_move_with_it_and_picks_stay(self):
         current = {"0": self.TOOL, "10": self.TOOL, "11": "GE-Proton11-7", "12": self.TOOL}
         auto = {"10": self.TOOL, "11": self.TOOL, "12": self.TOOL}
diff --git a/tools/tests/test_steam_compat_live.py b/tools/tests/test_steam_compat_live.py
index dfe76ce6..03331fc9 100644
--- a/tools/tests/test_steam_compat_live.py
+++ b/tools/tests/test_steam_compat_live.py
@@ -221,6 +221,187 @@ class ReconcileTest(unittest.TestCase):
         self.assertEqual(page.sets, [("10", TOOL_11), ("11", TOOL)])
         self.assertEqual(state["auto"], {"11": TOOL})
 
+    def test_native_arm64_title_drops_auto_proton_once_and_keeps_explicit_choices(self):
+        (self.steam / "steamapps/appmanifest_11.acf").unlink()
+        (self.state / "state.json").write_text(json.dumps({
+            "default": TOOL,
+            "auto": {"10": TOOL},
+        }))
+        page = FakePage({"0": TOOL, "10": TOOL}, [TOOL, TOOL_11])
+        original_native_targets = COMPAT["native_targets"]
+        COMPAT["native_targets"] = lambda _root, _apps: {"10": None}
+        try:
+            state = self.reconcile(page)
+            self.assertEqual(page.sets, [("10", "")])
+            self.assertEqual(page.mapping["10"], "")
+            self.assertEqual(state["auto"], {})
+
+            page.sets.clear()
+            self.reconcile(page)
+            self.assertEqual(page.sets, [])
+
+            (self.state / "games.json").write_text(json.dumps({
+                "version": 1,
+                "games": {"10": {"valve": True, "dir": "Proton 11.0 (ARM64)"}},
+            }))
+            state = self.reconcile(page)
+            self.assertEqual(page.sets, [("10", TOOL_11)])
+            self.assertEqual(page.mapping["10"], TOOL_11)
+            self.assertEqual(state["auto"], {})
+            (self.state / "games.json").unlink()
+
+            page.sets.clear()
+            page.mapping["10"] = "steamlinuxruntime_arm64"
+            self.reconcile(page)
+            self.assertEqual(page.mapping["10"], "steamlinuxruntime_arm64")
+            self.assertEqual(page.sets, [])
+
+            page.mapping["10"] = TOOL_11
+            self.reconcile(page)
+            self.assertEqual(page.mapping["10"], TOOL_11)
+            self.assertEqual(page.sets, [])
+
+            page.mapping["10"] = COMPAT["FEX_TOOL"]
+            self.reconcile(page)
+            self.assertEqual(page.mapping["10"], COMPAT["FEX_TOOL"])
+            self.assertEqual(page.sets, [])
+
+            page.mapping["10"] = "GE-Proton11-7"
+            self.reconcile(page)
+            self.assertEqual(page.mapping["10"], "GE-Proton11-7")
+            self.assertEqual(page.sets, [])
+        finally:
+            COMPAT["native_targets"] = original_native_targets
+
+    def test_factorio_native_choice_survives_inherited_live_selection_and_restart(self):
+        app = "427520"
+        (self.steam / ("steamapps/appmanifest_%s.acf" % app)).write_text("")
+        config = self.steam / "config/config.vdf"
+        config.parent.mkdir(parents=True)
+        config.write_text(
+            '"InstallConfigStore" { "Software" { "Valve" { "Steam" { '
+            '"CompatToolMapping" { "0" { "name" "%s" } } } } } }' % TOOL)
+        (self.state / "state.json").write_text(json.dumps({
+            "default": TOOL,
+            "auto": {app: TOOL},
+        }))
+
+        original_native_targets = COMPAT["native_targets"]
+        COMPAT["native_targets"] = lambda _root, apps: {
+            app: COMPAT["NATIVE_CHOICE"]
+        } if app in apps else {}
+        try:
+            page = FakePage({"0": TOOL, "10": TOOL, "11": TOOL, app: "proton"}, [TOOL, TOOL_11])
+            state = self.reconcile(page)
+            self.assertEqual(page.sets, [])
+            self.assertEqual(state["auto"], {})
+            self.assertEqual(state["native"], [app])
+            self.assertEqual(COMPAT["read_config_mapping"](str(config)), {"0": TOOL})
+
+            page.sets.clear()
+            state = self.reconcile(page)
+            self.assertEqual(page.sets, [])
+            self.assertEqual(state["native"], [app])
+            restarted = LIVE["Helper"](str(self.steam), 1)
+            restarted.page = page
+            restarted.reconcile()
+            state = json.loads((self.state / "state.json").read_text())
+            self.assertEqual(page.sets, [])
+            self.assertEqual(state["native"], [app])
+
+            config.write_text(
+                '"InstallConfigStore" { "Software" { "Valve" { "Steam" { '
+                '"CompatToolMapping" { "0" { "name" "%s" } '
+                '"%s" { "name" "GE-Proton11-7" } } } } } }' % (TOOL, app))
+            page.mapping[app] = "GE-Proton11-7"
+            state = self.reconcile(page)
+            self.assertEqual(page.mapping[app], "GE-Proton11-7")
+            self.assertEqual(page.sets, [])
+            self.assertEqual(state["native"], [])
+
+            for choice in ("steamlinuxruntime", COMPAT["FEX_TOOL"], TOOL_11):
+                (self.state / "state.json").write_text(json.dumps({
+                    "default": TOOL,
+                    "auto": {},
+                    "native": [app],
+                }))
+                config.write_text(
+                    '"InstallConfigStore" { "Software" { "Valve" { "Steam" { '
+                    '"CompatToolMapping" { "0" { "name" "%s" } '
+                    '"%s" { "name" "%s" } } } } } }' % (TOOL, app, choice))
+                page.mapping[app] = choice
+                page.sets.clear()
+                state = self.reconcile(page)
+                self.assertEqual(page.mapping[app], choice)
+                self.assertEqual(page.sets, [])
+                self.assertEqual(state["native"], [], choice)
+        finally:
+            COMPAT["native_targets"] = original_native_targets
+
+    def test_saved_native_choice_survives_live_restart_without_manifest_or_appinfo(self):
+        app = "452280"
+        config = self.steam / "config/config.vdf"
+        config.parent.mkdir(parents=True)
+        config.write_text(
+            '"InstallConfigStore" { "Software" { "Valve" { "Steam" { '
+            '"CompatToolMapping" { "0" { "name" "%s" } } } } } }' % TOOL)
+        (self.state / "state.json").write_text(json.dumps({
+            "default": TOOL,
+            "auto": {},
+            "native": [app],
+        }))
+
+        original_native_targets = COMPAT["native_targets"]
+        COMPAT["native_targets"] = lambda _root, _apps: {}
+        try:
+            page = FakePage({"0": TOOL, app: "proton"}, [TOOL, TOOL_11])
+            state = self.reconcile(page)
+            self.assertNotIn(app, self.helper.installed)
+            self.assertEqual(state["native"], [app])
+            self.assertNotIn(app, state["auto"])
+            self.assertNotIn((app, TOOL), page.sets)
+            self.assertEqual(COMPAT["read_config_mapping"](str(config)), {"0": TOOL})
+
+            config.write_text('"InstallConfigStore" { "Software" { "Other" {} } }')
+            state = self.reconcile(page)
+            self.assertEqual(state["native"], [app])
+            self.assertNotIn((app, TOOL), page.sets)
+
+            config.write_text(
+                '"InstallConfigStore" { "Software" { "Valve" { "Steam" { '
+                '"CompatToolMapping" { "0" { "name" "%s" } '
+                '"%s" { "name" "GE-Proton11-7" } } } } } }' % (TOOL, app))
+            page.mapping[app] = "proton"
+            state = self.reconcile(page)
+            self.assertEqual(state["native"], [])
+            self.assertNotIn((app, TOOL), page.sets)
+            self.assertEqual(COMPAT["read_config_mapping"](str(config))[app], "GE-Proton11-7")
+        finally:
+            COMPAT["native_targets"] = original_native_targets
+
+    def test_factorio_without_prior_auto_state_uses_the_default_proton(self):
+        app = "427520"
+        (self.steam / ("steamapps/appmanifest_%s.acf" % app)).write_text("")
+        config = self.steam / "config/config.vdf"
+        config.parent.mkdir(parents=True)
+        config.write_text(
+            '"InstallConfigStore" { "Software" { "Valve" { "Steam" { '
+            '"CompatToolMapping" { "0" { "name" "%s" } } } } } }' % TOOL)
+        (self.state / "state.json").write_text(json.dumps({"default": TOOL, "auto": {}}))
+        page = FakePage({"0": TOOL, "10": TOOL, "11": TOOL, app: "proton"}, [TOOL, TOOL_11])
+        original_native_targets = COMPAT["native_targets"]
+        COMPAT["native_targets"] = lambda _root, apps: {
+            app: COMPAT["NATIVE_CHOICE"]
+        } if app in apps else {}
+        try:
+            state = self.reconcile(page)
+            self.assertEqual(page.sets, [(app, TOOL)])
+            self.assertEqual(state["auto"], {app: TOOL})
+            self.assertEqual(state["native"], [])
+            self.assertEqual(COMPAT["read_config_mapping"](str(config)), {"0": TOOL})
+        finally:
+            COMPAT["native_targets"] = original_native_targets
+
     def test_missing_per_game_proton_stays_deferred_live(self):
         page = FakePage({"0": TOOL, "10": "GE-Proton9-1", "11": TOOL_11}, [TOOL, TOOL_11])
         (self.state / "games.json").write_text(json.dumps({