diff --git a/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts b/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts
index 8fca16a101725..d477d80c72cb4 100644
--- a/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts
+++ b/apps/server/src/orchestration-v2/ProviderTurnStartService.test.ts
@@ -874,6 +874,63 @@ effectIt.effect("does not resume a continuation stopped while recovery was in fl
   }),
 );
 
+effectIt.effect.each([["node_modules"], ["node_modules", ".next"]])(
+  "recreates a managed worktree folder that holds only %s",
+  (leftovers) =>
+    Effect.gen(function* () {
+      const fileSystem = yield* FileSystem.FileSystem;
+      const path = yield* Path.Path;
+      const workspaceRoot = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-start-" });
+      const worktreePath = path.join(workspaceRoot, "project", "worktree");
+      // What a junction-skipping `git worktree remove` leaves behind: no `.git`, no files.
+      for (const leftover of leftovers) {
+        yield* fileSystem.makeDirectory(path.join(worktreePath, leftover), { recursive: true });
+      }
+      const harness = makeLocalCommandHarness({
+        text: "Continue",
+        worktreePath,
+        worktreesDir: workspaceRoot,
+        fileSystem,
+        failReadsAfterRunning: true,
+      });
+      // `git worktree add` refuses a non-empty target, so the leftover must be gone first.
+      harness.createWorktree.mockImplementation(() =>
+        fileSystem.exists(worktreePath).pipe(
+          Effect.tap((exists) => Effect.sync(() => expect(exists).toBe(false))),
+          Effect.as({} as never),
+          Effect.orDie,
+        ),
+      );
+      yield* harness.start;
+      expect(harness.createWorktree).toHaveBeenCalledWith({
+        cwd: "/tmp/native-account-project",
+        refName: "feature/restore",
+        path: worktreePath,
+      });
+    }).pipe(Effect.scoped, Effect.provide(NodeServices.layer)),
+);
+
+effectIt.effect("leaves a managed worktree folder with other files untouched", () =>
+  Effect.gen(function* () {
+    const fileSystem = yield* FileSystem.FileSystem;
+    const path = yield* Path.Path;
+    const workspaceRoot = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-start-" });
+    const worktreePath = path.join(workspaceRoot, "project", "worktree");
+    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: workspaceRoot,
+      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.each(["cleanup-first", "startup-first"])(
   "coordinates provider startup with %s",
   (order) =>
diff --git a/apps/server/src/orchestration-v2/ProviderTurnStartService.ts b/apps/server/src/orchestration-v2/ProviderTurnStartService.ts
index 4eb988ec43089..65abfef4678ce 100644
--- a/apps/server/src/orchestration-v2/ProviderTurnStartService.ts
+++ b/apps/server/src/orchestration-v2/ProviderTurnStartService.ts
@@ -69,6 +69,9 @@ export class ProviderTurnStartError extends Schema.TaggedError<ProviderTurnStart
 
 const isProviderTurnStartError = Schema.is(ProviderTurnStartError);
 
+// Folders `git worktree remove` can leave behind when they are junctions or locked.
+const LEFTOVER_WORKTREE_ENTRIES = new Set(["node_modules", ".next"]);
+
 /**
  * Claude refuses these before it reads the prompt: replacing a process running background work,
  * or launch arguments whose appended system prompt cannot be read.
@@ -490,7 +493,20 @@ export const layer: Layer.Layer<
         const exists = yield* fileSystem
           .exists(worktreePath)
           .pipe(Effect.orElseSucceed(() => true));
-        if (!exists && (yield* isManagedWorktreePath(worktreePath))) {
+        const managed = yield* isManagedWorktreePath(worktreePath);
+        // A `git worktree remove` that skips a junctioned `node_modules` leaves
+        // a folder with no checkout. Only that leftover is cleared, never user files.
+        const leftover =
+          exists &&
+          managed &&
+          !(yield* fileSystem
+            .exists(path.join(worktreePath, ".git"))
+            .pipe(Effect.orElseSucceed(() => true))) &&
+          (yield* fileSystem.readDirectory(worktreePath).pipe(
+            Effect.map((entries) => entries.every((entry) => LEFTOVER_WORKTREE_ENTRIES.has(entry))),
+            Effect.orElseSucceed(() => false),
+          ));
+        if (managed && (!exists || leftover)) {
           const project = yield* projects.getById(projection.thread.projectId).pipe(
             Effect.map(Option.getOrUndefined),
             Effect.orElseSucceed(() => undefined),
@@ -501,7 +517,10 @@ export const layer: Layer.Layer<
               worktreePath,
               branch,
             });
-            yield* gitWorkflow.pruneWorktrees({ cwd: project.workspaceRoot }).pipe(
+            yield* (
+              leftover ? fileSystem.remove(worktreePath, { recursive: true }) : Effect.void
+            ).pipe(
+              Effect.andThen(gitWorkflow.pruneWorktrees({ cwd: project.workspaceRoot })),
               Effect.andThen(
                 gitWorkflow.createWorktree({
                   cwd: project.workspaceRoot,
diff --git a/apps/server/src/storageCleanup.test.ts b/apps/server/src/storageCleanup.test.ts
index b8332de492884..388628d1e0fb4 100644
--- a/apps/server/src/storageCleanup.test.ts
+++ b/apps/server/src/storageCleanup.test.ts
@@ -664,6 +664,25 @@ it.live("preserves late tracked edits when submodules were never initialized", (
   ),
 );
 
+it.live("keeps a managed worktree folder left with only node_modules", () =>
+  runCleanupTest(
+    Effect.gen(function* () {
+      const { service, fs, repo, worktree, command } = yield* cleanupFixture();
+      yield* fs.makeDirectory(`${worktree}/node_modules/pkg`, { recursive: true });
+      for (const entry of yield* fs.readDirectory(worktree)) {
+        if (entry !== "node_modules") yield* fs.remove(`${worktree}/${entry}`, { recursive: true });
+      }
+      yield* command(repo, ["worktree", "prune"]);
+      const report = yield* service.runNow;
+      expect(report.entries.find((entry) => entry.path === worktree)).toMatchObject({
+        outcome: "kept",
+        reason: "Not a linked worktree",
+      });
+      expect(yield* fs.exists(`${worktree}/node_modules/pkg`)).toBe(true);
+    }),
+  ),
+);
+
 describe("subagent worktree ownership", () => {
   it.effect.each([
     "idle",
diff --git a/apps/server/src/storageCleanup.ts b/apps/server/src/storageCleanup.ts
index 471e78df2a3b1..52bc2185515e6 100644
--- a/apps/server/src/storageCleanup.ts
+++ b/apps/server/src/storageCleanup.ts
@@ -819,7 +819,8 @@ const make = Effect.gen(function* () {
           return keep("outside the managed worktree folder");
         if (yield* containsProjectRoot(worktreePath, [project, ...snapshot.projects]))
           return keep("contains a project checkout");
-        if ((yield* fs.stat(path.join(worktreePath, ".git"))).type !== "File")
+        const gitPath = path.join(worktreePath, ".git");
+        if (!(yield* fs.exists(gitPath)) || (yield* fs.stat(gitPath)).type !== "File")
           return keep("not a linked worktree");
         if (yield* branchChanged(worktreePath, thread.branch))
           return keep("repository or branch changed");