diff --git a/src/main/ipc/worktrees.test.ts b/src/main/ipc/worktrees.test.ts
index d61b92852e0..f7af28221bb 100644
--- a/src/main/ipc/worktrees.test.ts
+++ b/src/main/ipc/worktrees.test.ts
@@ -540,6 +540,22 @@ describe('registerWorktreeHandlers', () => {
     expect(handlers['worktrees:getBranchRenameFailureOutput']).toBeDefined()
   })
 
+  it('persistSortOrder only reorders existing worktrees and never mints meta for a stale id', () => {
+    const liveId = 'repo-1::/workspace/repo'
+    const staleId = 'removed-repo::/workspace/gone'
+    // Only the live worktree has meta; the stale id (e.g. a removed repo the
+    // renderer still lists) has none and must be skipped, not created.
+    store.getWorktreeMeta.mockImplementation((id: string) =>
+      id === liveId ? ({ instanceId: 'x' } as never) : undefined
+    )
+
+    handlers['worktrees:persistSortOrder'](null, { orderedIds: [liveId, staleId] })
+
+    const orderedTargets = store.setWorktreeMeta.mock.calls.map((call) => call[0])
+    expect(orderedTargets).toContain(liveId)
+    expect(orderedTargets).not.toContain(staleId)
+  })
+
   it('prefetches the local default create base through the runtime refresh cache', async () => {
     const repo = {
       id: 'repo-1',
diff --git a/src/main/ipc/worktrees.ts b/src/main/ipc/worktrees.ts
index 40cf7efd17d..5acd40c4f4d 100644
--- a/src/main/ipc/worktrees.ts
+++ b/src/main/ipc/worktrees.ts
@@ -2067,6 +2067,14 @@ export function registerWorktreeHandlers(
     }
     const now = Date.now()
     for (let i = 0; i < args.orderedIds.length; i++) {
+      // Why: a sidebar-order snapshot must only reorder worktrees that already
+      // exist — it must never create one. Without this guard a stale id the
+      // renderer still lists (e.g. a removed repo's `${repoId}::${path}`) gets a
+      // fresh worktreeMeta entry minted here, resurrecting an orphan/duplicate
+      // workspace on the next launch. setWorktreeMeta has no repo-existence check.
+      if (!store.getWorktreeMeta(args.orderedIds[i])) {
+        continue
+      }
       // Descending timestamps: first item gets highest sortOrder so b - a sorts first-wins on cold start.
       store.setWorktreeMeta(args.orderedIds[i], { sortOrder: now - i * 1000 })
     }
diff --git a/src/main/runtime/orca-runtime.ts b/src/main/runtime/orca-runtime.ts
index 08303980060..66765544e79 100644
--- a/src/main/runtime/orca-runtime.ts
+++ b/src/main/runtime/orca-runtime.ts
@@ -19973,6 +19973,12 @@ export class OrcaRuntimeService {
     const now = Date.now()
     let updated = 0
     for (let i = 0; i < orderedIds.length; i++) {
+      // Why: a sort-order snapshot must only reorder existing worktrees, never
+      // mint new meta — a stale id would otherwise resurrect an orphan workspace
+      // (setWorktreeMeta has no repo-existence check).
+      if (!this.store.getWorktreeMeta(orderedIds[i])) {
+        continue
+      }
       this.store.setWorktreeMeta(orderedIds[i], { sortOrder: now - i * 1000 })
       updated++
     }