diff --git a/server/src/__tests__/nested-clone-migration.test.ts b/server/src/__tests__/nested-clone-migration.test.ts
index e77222c4b9e..b417a4ce897 100644
--- a/server/src/__tests__/nested-clone-migration.test.ts
+++ b/server/src/__tests__/nested-clone-migration.test.ts
@@ -14,7 +14,7 @@ import { realizeExecutionWorkspace } from "../services/workspace-runtime.js";
 import { executionWorkspaceService } from "../services/execution-workspaces.js";
 import { prepareProjectRepositoryWorkspaces } from "../services/heartbeat/workspaces.js";
 import { expireReconstructableGitWorkspace } from "../services/git-workspace-expiration.js";
-import { currentRestorePointSnapshot } from "../services/git-restore-point.js";
+import { currentRestorePointSnapshot, restorePointHistoryDigest } from "../services/git-restore-point.js";
 import { nestedRepositoryBaseCandidates, nestedWorktreeBranchPrefix, readLinkedNestedCheckout, withNestedRepositoryBaseLock } from "../services/nested-repository-worktrees.js";
 import { listNestedCloneMigrationNames, migrateNestedRepositoryClone, nextNestedCloneMigrationBatch, type NestedCloneMigrationOptions } from "../services/nested-clone-migration.js";
 import { getStorageService } from "../storage/index.js";
@@ -225,6 +225,41 @@ describeEmbeddedPostgres("nested repository clone migration", () => {
     expect(git(f.checkout, "cat-file", "-t", feature)).toBe("commit");
   });
 
+  it("expires a converted checkout whose only extra history is remote-tracking and restores that history", async () => {
+    const f = await fixture({ issueStatus: "done" });
+    git(f.nested.author, "checkout", "-q", "-b", "squashed-away");
+    await fs.writeFile(path.join(f.nested.author, "feature.txt"), "feature\n");
+    git(f.nested.author, "add", "."); git(f.nested.author, "commit", "-qm", "Feature");
+    const feature = git(f.nested.author, "rev-parse", "HEAD");
+    git(f.nested.author, "push", "-q", f.nested.remote, "squashed-away");
+    git(f.checkout, "fetch", "-q", "origin");
+    git(f.nested.remote, "branch", "-D", "squashed-away");
+    git(f.nested.remote, "reflog", "expire", "--expire=now", "--all");
+    git(f.nested.remote, "gc", "-q", "--prune=now");
+    expect(await f.migrate()).toMatchObject({ outcome: "migrated" });
+
+    expect(await f.expire()).toMatchObject({ expired: true, restorePoint: true, skipReason: null });
+    for (const line of ownedRefs(f.base, f.prefix).split("\n").filter(Boolean)) git(f.base, "update-ref", "-d", line.split(" ")[0]!);
+    git(f.base, "reflog", "expire", "--expire=now", "--all");
+    git(f.base, "gc", "-q", "--prune=now");
+    expect(() => git(f.base, "cat-file", "-e", `${feature}^{commit}`)).toThrow();
+    expect(await f.reopen()).toMatchObject({ ok: true, reopened: true });
+    expect(git(f.checkout, "cat-file", "-t", feature)).toBe("commit");
+  });
+
+  it("fingerprints a converted checkout's own history rather than the shared clone's remote refs", async () => {
+    const f = await fixture();
+    expect(await f.migrate()).toMatchObject({ outcome: "migrated" });
+    const head = git(f.checkout, "rev-parse", "HEAD");
+    const before = await restorePointHistoryDigest(f.checkout);
+    git(f.base, "update-ref", "refs/remotes/origin/another-task", head);
+    expect(await restorePointHistoryDigest(f.checkout)).toBe(before);
+    git(f.base, "update-ref", `refs/heads/${f.prefix}remotes/origin/extra`, head);
+    expect(await restorePointHistoryDigest(f.checkout)).not.toBe(before);
+    for (let index = 0; index < 64; index++) git(f.base, "update-ref", `refs/heads/${f.prefix}remotes/origin/bulk-${index}`, head);
+    await expect(restorePointHistoryDigest(f.checkout)).rejects.toThrow("managed_checkout_local_tip_budget");
+  });
+
   it("finishes an interrupted conversion after the workspace is archived and forgets one whose workspace is gone", async () => {
     const f = await fixture();
     const { unpushed } = await nestedWork(f.checkout);
diff --git a/server/src/services/git-restore-point.ts b/server/src/services/git-restore-point.ts
index 698b1395ade..3af9997b693 100644
--- a/server/src/services/git-restore-point.ts
+++ b/server/src/services/git-restore-point.ts
@@ -595,9 +595,21 @@ export async function restorePointHistoryDigest(input: string, signal?: AbortSig
   const cwd = await fs.realpath(input);
   const reflog = await gitText(cwd, ["reflog", "show", "--format=%H", "HEAD"], { signal }).catch(() => "");
   const original = await gitText(cwd, ["rev-parse", "--verify", "-q", "ORIG_HEAD^{commit}"], { signal }).catch(() => "");
-  const remotes = await gitText(cwd, ["for-each-ref", "--format=%(objectname) %(refname)", "refs/remotes"], { signal }).catch(() => "");
-  const remoteReflogs = (await gitText(cwd, ["reflog", "show", "--all", "--format=%H %gD"], { signal }).catch(() => ""))
-    .split("\n").filter((line) => / refs\/remotes\//.test(line));
+  const linked = (await fs.lstat(path.join(cwd, ".git")).catch(() => null))?.isFile() ?? false;
+  const nested = linked ? await import("./nested-repository-worktrees.js") : null;
+  const scope = nested ? `refs/heads/${await nested.nestedWorktreeBranchPrefix(cwd)}` : "refs/remotes";
+  const remotes = await gitText(cwd, ["for-each-ref", ...nested ? [`--count=${nested.OWNED_NESTED_REF_LIMIT + 1}`] : [],
+    "--format=%(objectname) %(refname)", scope], { signal }).catch(() => "");
+  const remoteReflogs: string[] = [];
+  if (nested) {
+    if (remotes.split("\n").filter(Boolean).length > nested.OWNED_NESTED_REF_LIMIT) throw new Error("managed_checkout_local_tip_budget");
+    for (const ref of remotes.split("\n").map((line) => line.split(" ")[1]).filter(Boolean)) {
+      remoteReflogs.push(...(await gitText(cwd, ["reflog", "show", "--format=%H", ref!], { signal }).catch(() => "")).split("\n").filter((line) => SHA.test(line)).map((sha) => `${sha} ${ref}`));
+    }
+  } else {
+    remoteReflogs.push(...(await gitText(cwd, ["reflog", "show", "--all", "--format=%H %gD"], { signal }).catch(() => ""))
+      .split("\n").filter((line) => / refs\/remotes\//.test(line)));
+  }
   return createHash("sha256").update(JSON.stringify([reflog.split("\n").filter((line) => SHA.test(line)), SHA.test(original) ? original : null,
     remotes.split("\n").filter(Boolean), remoteReflogs])).digest("hex");
 }
diff --git a/server/src/services/git-workspace-restoration.ts b/server/src/services/git-workspace-restoration.ts
index f71c1851e7c..5aacb475a80 100644
--- a/server/src/services/git-workspace-restoration.ts
+++ b/server/src/services/git-workspace-restoration.ts
@@ -18,7 +18,7 @@ import { ensureGitRestorePointCommit, validateGitRestorePointRef, type GitRestor
 import { getStorageService } from "../storage/index.js";
 import type { StorageService } from "../storage/types.js";
 import { PROJECT_REPOSITORIES_DIR } from "@paperclipai/adapter-utils/git-workspace-sync";
-import { forgetExpiredNestedRepositoryWorktree, nestedRepositoryBaseCandidates, readLinkedNestedCheckout, recordedNestedRepositoryBase, type LinkedNestedCheckout } from "./nested-repository-worktrees.js";
+import { OWNED_NESTED_REF_LIMIT, forgetExpiredNestedRepositoryWorktree, nestedRepositoryBaseCandidates, readLinkedNestedCheckout, recordedNestedRepositoryBase, type LinkedNestedCheckout } from "./nested-repository-worktrees.js";
 
 const execFile = promisify(execFileCallback);
 const shaPattern = /^[a-f0-9]{40}$/;
@@ -249,7 +249,6 @@ async function assertCommitMessageSaved(cwd: string, gitDir: string, signal?: Ab
   if (!saved.includes(message.trim())) throw new Error("uncommitted_git_message");
 }
 
-const OWNED_NESTED_REF_LIMIT = 64;
 
 async function ownedNestedRefs(linked: LinkedNestedCheckout, signal?: AbortSignal) {
   const refs = (await gitCacheCommand(linked.checkout, ["for-each-ref", `--count=${OWNED_NESTED_REF_LIMIT + 1}`,
@@ -380,9 +379,13 @@ async function provenNestedWorktreeHistory(linked: LinkedNestedCheckout, repoUrl
   const covered = new Set([head,
     ...shas(await gitCacheCommand(checkout, ["reflog", "show", "--format=%H", "HEAD"], signal).catch(() => "")),
     ...shas(await gitCacheCommand(checkout, ["rev-parse", "--verify", "-q", "ORIG_HEAD^{commit}"], signal).catch(() => ""))]);
-  const owned = await ownedNestedRefs(linked, signal);
+  const allOwned = await ownedNestedRefs(linked, signal);
+  const remotePrefix = `refs/heads/${linked.branchPrefix}remotes/`;
+  const owned = allOwned.filter(([, ref]) => !ref.startsWith(remotePrefix));
+  const remoteTracked = [...new Set([...allOwned.filter(([, ref]) => ref.startsWith(remotePrefix)).map(([sha]) => sha),
+    ...await ownedNestedReflogs(linked, allOwned.filter(([, ref]) => ref.startsWith(remotePrefix)), signal)])];
   const recorded = new Set([...owned.map(([sha]) => sha), ...await ownedNestedReflogs(linked, owned, signal)]);
-  if (recorded.size + covered.size > MANAGED_CHECKOUT_LOCAL_TIP_LIMIT) throw new Error("managed_checkout_local_tip_budget");
+  if (recorded.size + covered.size + remoteTracked.length > MANAGED_CHECKOUT_LOCAL_TIP_LIMIT) throw new Error("managed_checkout_local_tip_budget");
   const current = (await gitCacheCommand(checkout, ["symbolic-ref", "--quiet", "HEAD"], signal).catch(() => "")).trim();
   const otherTips = owned.filter(([, ref]) => ref !== current).map(([sha]) => sha);
   if (otherTips.length && await hasCommitsMissingUpstream(checkout, otherTips, repoUrl, resolveGitAuth, signal, [head])) {
@@ -393,7 +396,9 @@ async function provenNestedWorktreeHistory(linked: LinkedNestedCheckout, repoUrl
     throw new Error("unpushed_managed_checkout_branches");
   }
   const headOnRemote = !await hasCommitsMissingUpstream(checkout, [head], repoUrl, resolveGitAuth, signal);
-  return { headOnRemote, preserve: [] };
+  const preserve = remoteTracked.length
+    ? await tipsMissingUpstream(checkout, remoteTracked, repoUrl, resolveGitAuth, signal, [...covered, ...recorded]) : [];
+  return { headOnRemote, preserve };
 }
 
 async function tipsMissingUpstream(checkout: string, tips: string[], repoUrl: string,
diff --git a/server/src/services/nested-repository-worktrees.ts b/server/src/services/nested-repository-worktrees.ts
index 8a2969ec2f3..ad907159cc3 100644
--- a/server/src/services/nested-repository-worktrees.ts
+++ b/server/src/services/nested-repository-worktrees.ts
@@ -15,6 +15,7 @@ import { sanitizeRuntimeServiceBaseEnv } from "./runtime-service-env.js";
 const execFile = promisify(execFileCallback);
 const NESTED_WORKTREE_GIT_TIMEOUT_MS = 10 * 60 * 1000;
 const NESTED_WORKTREE_BRANCH = /^paperclip\/[a-f0-9]{12}\/./;
+export const OWNED_NESTED_REF_LIMIT = 64;
 export const DETACHED_REPOSITORIES_DIR = path.join(".paperclip-runtime", "detached-repositories");
 
 export type LinkedNestedCheckout = { checkout: string; base: string; gitDir: string; admin: string; branchPrefix: string };