diff --git a/server/src/__tests__/environment-retained-orphan-sandbox.test.ts b/server/src/__tests__/environment-retained-orphan-sandbox.test.ts
index 66e4d2926d2..8c7b329bf6f 100644
--- a/server/src/__tests__/environment-retained-orphan-sandbox.test.ts
+++ b/server/src/__tests__/environment-retained-orphan-sandbox.test.ts
@@ -21,7 +21,7 @@ import { heartbeatService, type HeartbeatEnvironmentRuntime } from "../services/
 import { hasRecoveredCleanupStopReceipt } from "../services/remote-execution-termination.js";
 import { taskChatRetryExecutionStopped } from "../services/chat-channels/task-retry-authority.js";
 import { createOwnershipReportState, runOwnershipReconciliationPass } from "../services/recovery/ownership-invariant-report.js";
-import { ORPHANED_SANDBOX_RECOVERY_KEY } from "../services/sandbox-stop-and-retain.js";
+import { ORPHANED_SANDBOX_RECOVERY_KEY, settleStopOnlyCleanup } from "../services/sandbox-stop-and-retain.js";
 
 const support = await getEmbeddedPostgresTestSupport();
 const suite = support.supported ? describe : describe.skip;
@@ -111,6 +111,37 @@ suite("retained orphan sandbox on the shared ownership path", () => {
       recoveredOrphanedRunLease: true, ownerProof: "pid_dead", runId });
   });
 
+  it("keeps the orphan marker for a stop intent saved before the top-level marker existed", async () => {
+    const runId = await run("failed");
+    const id = randomUUID(), providerLeaseId = `sandbox://fake/${id}`, attemptId = randomUUID();
+    const intent = { schema: "paperclip.sandbox-stop-and-retain.v1", requestId: attemptId, companyId, runId, leaseId: id,
+      provider: "fake", providerLeaseId, builtinProvider: "fake", recoveredOrphanedRunLease: true, ownerProof: "pid_dead" };
+    await db.insert(environmentLeases).values({ id, companyId, environmentId, issueId, heartbeatRunId: runId,
+      status: "pending_cleanup", cleanupStatus: "failed", failureReason: "sandbox_stop_pending", leasePolicy: "ephemeral",
+      provider: "fake", providerLeaseId, metadata: { sandboxStopAndRetain: intent, pendingCleanupAttemptId: attemptId,
+        pendingCleanupInFlight: true } });
+    const settled = await settleStopOnlyCleanup(db, await row(id), { attemptId, receipt: { providerLeaseId, state: "stopped" } });
+    expect(settled).toMatchObject({ status: "released", cleanupStatus: "success" });
+    expect(settled?.metadata?.[ORPHANED_SANDBOX_RECOVERY_KEY]).toMatchObject({ recoveredOrphanedRunLease: true,
+      ownerProof: "pid_dead", runId, fromStopIntent: true });
+    const { kind } = await pass();
+    expect(kind).toMatchObject({ settled: 1 });
+    expect((await row(id))).toMatchObject({ status: "pending_cleanup", failureReason: "retained_orphan_sandbox_released" });
+  });
+
+  it("does not mark an ordinary stop-and-retain as an orphan", async () => {
+    const runId = await run("failed");
+    const id = randomUUID(), providerLeaseId = `sandbox://fake/${id}`, attemptId = randomUUID();
+    const intent = { schema: "paperclip.sandbox-stop-and-retain.v1", requestId: attemptId, companyId, runId, leaseId: id,
+      provider: "fake", providerLeaseId, builtinProvider: "fake" };
+    await db.insert(environmentLeases).values({ id, companyId, environmentId, issueId, heartbeatRunId: runId,
+      status: "pending_cleanup", cleanupStatus: "failed", leasePolicy: "ephemeral", provider: "fake", providerLeaseId,
+      metadata: { sandboxStopAndRetain: intent, pendingCleanupAttemptId: attemptId, pendingCleanupInFlight: true } });
+    const settled = await settleStopOnlyCleanup(db, await row(id), { attemptId, receipt: { providerLeaseId, state: "stopped" } });
+    expect(settled?.metadata?.[ORPHANED_SANDBOX_RECOVERY_KEY]).toBeUndefined();
+    expect((await pass()).kind).toMatchObject({ settled: 0 });
+  });
+
   it("destroys a retained orphan that nothing references, through the cleanup sweep", async () => {
     const leaseId = await retainedOrphan(await run("failed"));
     const { kind } = await pass();
diff --git a/server/src/services/sandbox-stop-and-retain.ts b/server/src/services/sandbox-stop-and-retain.ts
index a1ccefc1d6d..6269ed3b59d 100644
--- a/server/src/services/sandbox-stop-and-retain.ts
+++ b/server/src/services/sandbox-stop-and-retain.ts
@@ -184,6 +184,10 @@ export async function settleStopOnlyCleanup(db: Db, lease: Lease, options: { att
   const receipt = remoteTerminationReceipt(lease, options.receipt), stopped = receipt?.state === "stopped";
   const now = new Date();
   const removeIntent: SQL = stopped ? sql`- 'sandboxStopAndRetain'` : sql``;
+  const recordedIntent = lease.metadata?.[SANDBOX_STOP_AND_RETAIN_KEY] as Record<string, unknown> | undefined;
+  const legacyOrphan = stopped && recordedIntent?.recoveredOrphanedRunLease === true && !lease.metadata?.[ORPHANED_SANDBOX_RECOVERY_KEY]
+    ? { [ORPHANED_SANDBOX_RECOVERY_KEY]: { recoveredOrphanedRunLease: true, ownerProof: recordedIntent.ownerProof ?? null,
+      runId: lease.heartbeatRunId, recoveredAt: now.toISOString(), fromStopIntent: true } } : {};
   const [updated] = await writeEnvironmentCleanup(db, async tx => {
     if (stopped) await notifyRetainedNativeSessionCleanup(tx, { companyId: lease.companyId, runId: lease.heartbeatRunId! });
     return tx.update(environmentLeases).set({
@@ -199,6 +203,7 @@ export async function settleStopOnlyCleanup(db: Db, lease: Lease, options: { att
             : { builtinProvider: lease.provider, method: "builtin.stopLease" }),
           confirmedAt: receipt.confirmedAt,
         } } : {}),
+        ...legacyOrphan,
         pendingCleanupInFlight: false, pendingCleanupLeaseExpiresAtMs: 0,
       })}::jsonb`,
     }).where(stopOnlyAttempt(lease, options.attemptId)).returning();