diff --git a/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts b/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts
index 62f095b6fd913..efb12a224e015 100644
--- a/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts
+++ b/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts
@@ -1127,6 +1127,8 @@ effectIt.effect(
 
       const expectedTips = {
         retained: { tip: threadTip, file: "thread.txt", upstream: null, base: "" },
+        // A failed removal can leave the folder behind with only dependencies inside.
+        leftover: { tip: threadTip, file: "thread.txt", upstream: null, base: "" },
         deleted: { tip: projectTip, file: "project.txt", upstream: null, base: "project-current" },
         pushed: {
           tip: threadTip,
@@ -1171,7 +1173,12 @@ effectIt.effect(
           yield* git(workspaceRoot, ["remote", "remove", "origin"]);
         }
         yield* fileSystem.remove(worktreePath, { recursive: true });
-        if (scenario !== "retained") {
+        if (scenario === "leftover") {
+          yield* fileSystem.makeDirectory(path.join(worktreePath, "node_modules"), {
+            recursive: true,
+          });
+        }
+        if (scenario !== "retained" && scenario !== "leftover") {
           yield* git(workspaceRoot, ["worktree", "prune"]);
           yield* git(workspaceRoot, ["branch", "-D", "feature/restore"]);
         }
@@ -1220,6 +1227,27 @@ effectIt.effect(
     }).pipe(Effect.scoped, Effect.provide(layerRealGit)),
 );
 
+effectIt.effect("leaves a managed worktree folder without .git that holds user files", () =>
+  Effect.gen(function* () {
+    const fileSystem = yield* FileSystem.FileSystem;
+    const path = yield* Path.Path;
+    const worktreesDir = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-leftover-" });
+    const worktreePath = path.join(worktreesDir, "project", "restore");
+    yield* fileSystem.makeDirectory(path.join(worktreePath, "node_modules"), { recursive: true });
+    yield* fileSystem.writeFileString(path.join(worktreePath, "notes.md"), "keep me");
+    const harness = makeLocalCommandHarness({
+      text: "Continue",
+      worktreePath,
+      worktreesDir,
+      fileSystem,
+      failReadsAfterRunning: true,
+    });
+    yield* harness.start;
+    expect(harness.createWorktree).not.toHaveBeenCalled();
+    expect(yield* fileSystem.readFileString(path.join(worktreePath, "notes.md"))).toBe("keep me");
+  }).pipe(Effect.scoped, Effect.provide(NodeServices.layer)),
+);
+
 effectIt.effect(
   "preserves recreation interrupts and retries, then fails the final attempt before provider start",
   () =>
diff --git a/apps/server/src/storageCleanup.test.ts b/apps/server/src/storageCleanup.test.ts
index 28d66e50bb0bb..b0641a20428ec 100644
--- a/apps/server/src/storageCleanup.test.ts
+++ b/apps/server/src/storageCleanup.test.ts
@@ -2332,6 +2332,24 @@ describe("storage cleanup reports and local file policies", () => {
       }),
     ),
   );
+  it.effect("keeps a thread's worktree folder that lost its .git link", () =>
+    runCleanupTest(
+      Effect.gen(function* () {
+        yield* TestClock.setTime(NOW_MS);
+        const fixture = yield* cleanupFixture();
+        fixture.setThreads([
+          shell({ branch: "feature", worktreePath: fixture.worktree, archivedAt: at(-DAY_MS) }),
+        ]);
+        yield* fixture.fs.remove(`${fixture.worktree}/.git`);
+        yield* fixture.fs.makeDirectory(`${fixture.worktree}/node_modules`);
+        const report = yield* fixture.service.runNow;
+        expect(report.entries).toEqual([
+          expect.objectContaining({ path: fixture.worktree, outcome: "kept" }),
+        ]);
+        expect(yield* fixture.fs.exists(`${fixture.worktree}/node_modules`)).toBe(true);
+      }),
+    ),
+  );
   it.live("skips a stored worktree path whose parent is a regular file", () =>
     runCleanupTest(
       Effect.gen(function* () {
diff --git a/apps/server/src/storageCleanup.ts b/apps/server/src/storageCleanup.ts
index 0cf5eca0b80d0..99097501d49d7 100644
--- a/apps/server/src/storageCleanup.ts
+++ b/apps/server/src/storageCleanup.ts
@@ -1010,8 +1010,10 @@ const make = Effect.gen(function* () {
         return "worktree is a symbolic link";
       if (!roots.some((root) => inside(root, realPath)))
         return "outside the managed worktree folder";
-      if ((yield* fs.stat(path.join(worktreePath, ".git"))).type !== "File")
-        return "not a linked worktree";
+      const gitLink = yield* fs
+        .stat(path.join(worktreePath, ".git"))
+        .pipe(Effect.catchReason("PlatformError", "NotFound", () => Effect.undefined));
+      if (gitLink?.type !== "File") return "not a linked worktree";
       return null;
     });
     const deletedRows = yield* sql<{ payload_json: string; workspaceRoot: string }>`
diff --git a/apps/server/src/workspace/restoreMissingWorktree.ts b/apps/server/src/workspace/restoreMissingWorktree.ts
index ee423c47d06ab..4bc1ac8f533c8 100644
--- a/apps/server/src/workspace/restoreMissingWorktree.ts
+++ b/apps/server/src/workspace/restoreMissingWorktree.ts
@@ -33,6 +33,9 @@ class WorktreeRecreateNoBaseError extends Schema.TaggedError<WorktreeRecreateNoB
   }
 }
 
+// `git worktree remove` skips pnpm junctions on Windows, leaving these behind without a checkout.
+const LEFTOVER_WORKTREE_ENTRIES = new Set(["node_modules", ".next"]);
+
 interface WorktreeThread {
   readonly id: ThreadId;
   readonly projectId: ProjectId;
@@ -42,10 +45,33 @@ interface WorktreeThread {
 
 export const makeRestoreMissingWorktree = Effect.gen(function* () {
   const fileSystem = yield* FileSystem.FileSystem;
+  const path = yield* Path.Path;
   const gitWorkflow = yield* GitWorkflowService.GitWorkflowService;
   const projects = yield* ProjectService.ProjectService;
   const isManagedWorktreePath = yield* makeIsManagedWorktreePath;
 
+  // Only folders holding nothing but leftovers are cleared, never user files.
+  const isLeftoverFolder = (worktreePath: string) =>
+    fileSystem.exists(path.join(worktreePath, ".git")).pipe(
+      Effect.flatMap((hasGit) =>
+        hasGit
+          ? Effect.succeed(false)
+          : fileSystem.readDirectory(worktreePath).pipe(
+              Effect.flatMap((entries) =>
+                Effect.forEach(entries, (entry) =>
+                  LEFTOVER_WORKTREE_ENTRIES.has(entry)
+                    ? fileSystem
+                        .stat(path.join(worktreePath, entry))
+                        .pipe(Effect.map((info) => info.type === "Directory"))
+                    : Effect.succeed(false),
+                ),
+              ),
+              Effect.map((leftovers) => leftovers.every(Boolean)),
+            ),
+      ),
+      Effect.orElseSucceed(() => false),
+    );
+
   const resolveRecreateBase = Effect.fn("restoreMissingWorktree.resolveRecreateBase")(function* (
     cwd: string,
     remoteName: string | null,
@@ -116,7 +142,8 @@ export const makeRestoreMissingWorktree = Effect.gen(function* () {
     const { worktreePath, branch } = thread;
     if (worktreePath === null || branch === null) return;
     const exists = yield* fileSystem.exists(worktreePath).pipe(Effect.orElseSucceed(() => true));
-    if (exists || !(yield* isManagedWorktreePath(worktreePath))) return;
+    const leftover = exists && (yield* isLeftoverFolder(worktreePath));
+    if ((exists && !leftover) || !(yield* isManagedWorktreePath(worktreePath))) return;
     const project = yield* projects.getById(thread.projectId).pipe(
       Effect.map(Option.getOrUndefined),
       Effect.orElseSucceed(() => undefined),
@@ -127,7 +154,9 @@ export const makeRestoreMissingWorktree = Effect.gen(function* () {
       worktreePath,
       branch,
     });
-    yield* recreateMissingWorktree({ cwd: project.workspaceRoot, worktreePath, branch }).pipe(
+    // `git worktree add` refuses a non-empty target.
+    yield* (leftover ? fileSystem.remove(worktreePath, { recursive: true }) : Effect.void).pipe(
+      Effect.andThen(recreateMissingWorktree({ cwd: project.workspaceRoot, worktreePath, branch })),
       Effect.mapError((cause) =>
         cause._tag === "WorktreeRecreateNoBaseError"
           ? cause