diff --git a/apps/server/src/storageCleanup.test.ts b/apps/server/src/storageCleanup.test.ts
index de1ccfefcf64f..c3c7c27bc4b23 100644
--- a/apps/server/src/storageCleanup.test.ts
+++ b/apps/server/src/storageCleanup.test.ts
@@ -632,8 +632,26 @@ const submoduleCleanupFixture = () =>
 it.live("removes clean submodules recursively, including deinitialized repositories", () =>
   runCleanupTest(
     Effect.gen(function* () {
-      const { service, fs, repo, worktree, submodule, command, recordSubmodules } =
-        yield* submoduleCleanupFixture();
+      const fs = yield* FileSystem.FileSystem;
+      const git = yield* GitVcsDriver.GitVcsDriver;
+      let editedDuringClean = false;
+      const { service, repo, worktree, submodule, command, recordSubmodules, setPolicy } =
+        yield* submoduleCleanupFixture().pipe(
+          Effect.provideService(GitVcsDriver.GitVcsDriver, {
+            ...git,
+            execute: (input) =>
+              git.execute(input).pipe(
+                Effect.tap(() => {
+                  if (input.args[0] !== "clean") return Effect.void;
+                  editedDuringClean = true;
+                  return fs.writeFileString(`${input.cwd}/tracked.txt`, "late edit\n");
+                }),
+              ),
+          }),
+        );
+      setPolicy("tracked-changes");
+      yield* fs.writeFileString(`${worktree}/notes.txt`, "untracked\n");
+      yield* fs.writeFileString(`${worktree}/.env`, "ignored\n");
       yield* command(submodule, [
         "-c",
         "protocol.file.allow=always",
@@ -646,6 +664,7 @@ it.live("removes clean submodules recursively, including deinitialized repositor
       yield* command(submodule, ["submodule", "deinit", "stored"]);
       const admin = (yield* command(worktree, ["rev-parse", "--absolute-git-dir"])).stdout.trim();
       const report = yield* service.runNow;
+      expect(editedDuringClean).toBe(false);
       expect(report.entries.find((entry) => entry.path === worktree)).toMatchObject({
         outcome: "removed",
       });
@@ -751,15 +770,21 @@ it.live("keeps unpushed submodule history after checkout and deinitialization",
 it.live("keeps submodules when stored repository metadata is malformed", () =>
   runCleanupTest(
     Effect.gen(function* () {
-      const { service, fs, worktree, submodule, child, command } = yield* submoduleCleanupFixture();
+      const { service, fs, worktree, submodule, child, command, setPolicy } =
+        yield* submoduleCleanupFixture();
+      setPolicy("tracked-changes");
       const childGit = (yield* command(child, ["rev-parse", "--absolute-git-dir"])).stdout.trim();
       yield* command(submodule, ["submodule", "deinit", "child"]);
       yield* fs.writeFileString(`${childGit}/HEAD`, "not a ref\n");
+      yield* fs.writeFileString(`${worktree}/notes.txt`, "keep while the worktree stays\n");
       expect(
         (yield* service.runNow).entries.find((entry) => entry.path === worktree),
       ).toMatchObject({ outcome: "kept", reason: expect.stringContaining("inspected") });
       expect(yield* fs.exists(worktree)).toBe(true);
       expect(yield* fs.readFileString(`${childGit}/HEAD`)).toBe("not a ref\n");
+      expect(yield* fs.readFileString(`${worktree}/notes.txt`)).toBe(
+        "keep while the worktree stays\n",
+      );
     }),
   ),
 );
diff --git a/apps/server/src/storageCleanup.ts b/apps/server/src/storageCleanup.ts
index a5f9cd7eefa12..f062a04e7dfaf 100644
--- a/apps/server/src/storageCleanup.ts
+++ b/apps/server/src/storageCleanup.ts
@@ -1206,15 +1206,15 @@ const make = Effect.gen(function* () {
               )
             )
               return keep("settings changed since check");
-            // Clean only untracked files. Ordinary worktrees retain Git's final tracked-edit check.
-            if (settings.worktreeKeepWhen === "tracked-changes")
-              yield* cleanupGit(worktreePath, ["clean", "-ffdx"], "git clean");
             const submodules = yield* submoduleRemoval(worktreePath, settings);
             if (submodules.reason !== null) return keep(submodules.reason);
             if (submodules.force) {
               const changes = yield* localChangesReason(worktreePath, settings);
               if (changes !== null) return keep(changes);
             }
+            // Forced removal already discards local files; do not widen its final-check window.
+            if (settings.worktreeKeepWhen === "tracked-changes" && !submodules.force)
+              yield* cleanupGit(worktreePath, ["clean", "-ffdx"], "git clean");
             yield* removeLinkedWorktree({
               operation: "StorageCleanup.cleanupGit",
               cwd: project.workspaceRoot,