diff --git a/apps/api/src/services/config/config_profile_resolver.py b/apps/api/src/services/config/config_profile_resolver.py
index e04f164..e1f24d3 100644
--- a/apps/api/src/services/config/config_profile_resolver.py
+++ b/apps/api/src/services/config/config_profile_resolver.py
@@ -515,7 +515,13 @@ def apply_resolved_profile(
     files_dir = profile_dir / "files"
     mounts_dir = profile_dir / "mounts"
 
-    def write_canonical_file(root: Path, relative_path: str, content: str) -> Path | None:
+    def write_canonical_file(
+        root: Path,
+        relative_path: str,
+        content: str,
+        *,
+        preserve_inode: bool = False,
+    ) -> Path | None:
         path = root / relative_path
         try:
             path.resolve().relative_to(root.resolve())
@@ -523,6 +529,12 @@ def apply_resolved_profile(
             logger.warning("Profile file path escapes canonical storage: %s", relative_path)
             return None
         path.parent.mkdir(parents=True, exist_ok=True)
+        if preserve_inode and path.is_file():
+            # A file bind mount follows its inode, not its directory entry.
+            # Replacing this path would leave a running container attached to
+            # the old inode, so overwrite the existing file in place.
+            path.write_text(content, encoding="utf-8")
+            return path
         with tempfile.NamedTemporaryFile(
             mode="w", encoding="utf-8", dir=path.parent, delete=False
         ) as temporary_file:
@@ -534,7 +546,9 @@ def apply_resolved_profile(
     # Top-level profile files are individual bind mounts under the working
     # directory. They therefore cannot mask the workspace directory itself.
     for file_path, content in resolved.files.items():
-        canonical_file = write_canonical_file(files_dir, file_path, content)
+        canonical_file = write_canonical_file(
+            files_dir, file_path, content, preserve_inode=True
+        )
         if canonical_file is None:
             continue
         volume_mounts.append(
diff --git a/apps/api/tests/unit/test_config_profile_resolver.py b/apps/api/tests/unit/test_config_profile_resolver.py
index 9c9ee70..b0e94a6 100644
--- a/apps/api/tests/unit/test_config_profile_resolver.py
+++ b/apps/api/tests/unit/test_config_profile_resolver.py
@@ -36,7 +36,7 @@ class TestMergeFunctions:
 
     def test_merge_env_vars_tracks_overrides(self) -> None:
         """Test that env var overrides are tracked."""
-        overrides = {}
+        overrides: dict[str, str] = {}
         _merge_env_vars(
             {"A": "1"},
             {"A": "2"},
@@ -93,7 +93,7 @@ class TestMergeFunctions:
         """Test that mount mode conflicts are resolved (later wins)."""
         from src.services.config.config_profile_resolver import ResolvedMount
 
-        overrides = {}
+        overrides: dict[str, str] = {}
         result = _merge_mounts(
             {"/app": ResolvedMount(target="/app", mode="rw", files={})},
             [{"target": "/app", "mode": "ro", "files": {}}],
@@ -562,6 +562,28 @@ class TestApplyResolvedProfile:
         ]
         assert canonical_file.read_text() == "setting = true"
 
+    def test_top_level_file_update_preserves_bind_mount_inode(self, tmp_path) -> None:
+        """An individually bind-mounted file must update in place."""
+        profile_id = uuid.uuid4()
+        instance_root = tmp_path / "instances"
+        resolved = ResolvedProfile(
+            profile_id=profile_id,
+            profile_name="test",
+            files={"settings.toml": "value = 1"},
+        )
+
+        apply_resolved_profile(str(instance_root / "instance-a"), resolved)
+        canonical_file = (
+            instance_root / "config-profiles" / str(profile_id) / "files" / "settings.toml"
+        )
+        original_inode = canonical_file.stat().st_ino
+
+        resolved.files["settings.toml"] = "value = 2"
+        apply_resolved_profile(str(instance_root / "instance-a"), resolved)
+
+        assert canonical_file.stat().st_ino == original_inode
+        assert canonical_file.read_text() == "value = 2"
+
     def test_instances_share_profile_scoped_mount_sources(self, tmp_path) -> None:
         """Different instance paths resolve a profile to one canonical source."""
         profile_id = uuid.uuid4()