Codex Desktop bug report: recent conversation history hidden/stale despite local DB containing threads

[ealdent]

What version of the Codex App are you using (From “About Codex” dialog)?

26.429.30905

What subscription do you have?

Pro

What platform is your computer?

Darwin 25.4.0 arm64 arm

What issue are you seeing?

Codex Desktop appears to show a stale or incorrectly filtered conversation sidebar after recent CLI/extension/app history imports. Recent conversations exist in the local Codex state database and are returned by the app-server thread/list API, but the Desktop UI does not show them. Manual repairs to global/sidebar state are overwritten on app startup.

The issue appears related to the Desktop "Imported agent setup" flow. I clicked the "Import again" button multiple times. The visible badge count decreased from 16 to 0, and the card reported "Last imported 16h ago", but the sidebar remained stale after repeated imports and after restarting the app.

Impact: I experience this as lost conversation history. Multiple recent project conversations are missing from the visible sidebar, especially recent Mother OS and BlueChimp work. The sidebar appears to show conversations up to roughly 14-16 hours ago, then jumps to much older history, despite the database containing many conversations in between.

Environment:

• Product: Codex Desktop app on macOS
• Platform: Darwin 25.4.0 arm64 arm
• Observed app version from process metadata: 26.429.30905
• Electron version from process metadata: 41.2.0
• Local Codex state database: ~/.codex/state_5.sqlite
• Global UI state file: ~/.codex/.codex-global-state.json
• Global UI state backup file: ~/.codex/.codex-global-state.json.bak

Evidence:

• Local DB contains the missing recent conversations with archived = 0.
• A direct app-server thread/list request with limit: 30, sortKey: "updated_at", sortDirection: "desc", archived: false, and useStateDbOnly: true returned the expected recent list, including the missing Mother OS and BlueChimp conversations.
• This suggests the database and app-server listing path are correct, while the Desktop sidebar display/state path is stale or filtered incorrectly.

Current hypothesis:
Codex Desktop startup or sidebar state reconciliation is restoring stale selected-remote-host-id and active-workspace-roots from app memory, migration logic, or another source of truth even after both global state files are repaired. This stale active project/remote state appears to affect the visible conversation list, while the underlying DB and app-server recent conversation API remain correct.

What steps can reproduce the bug?

1. Click the Desktop "Imported agent setup" / "Import again" action multiple times.
2. Observe the import badge count decrease from 16 to 0, suggesting the importer believes it processed the pending items.
3. Restart Codex Desktop.
4. Observe that the sidebar still shows stale history with recent conversations missing.
5. Inspect ~/.codex/state_5.sqlite and confirm the missing threads exist and are not archived.
6. Run PRAGMA integrity_check; it returns ok.
7. Query app-server thread/list with state DB only and confirm the missing conversations are returned.
8. Inspect global UI state and observe stale state similar to:

{
  "selected-remote-host-id": "[redacted remote host id]",
  "active-workspace-roots": ["[redacted stale workspace root]"],
  "electron-persisted-atom-state": {
    "sidebar-workspace-filter-v2": "all",
    "sidebar-organize-mode-v1": "recent",
    "sidebar-keep-projects-in-recent-v1": false
  }
}

9. Edit ~/.codex/.codex-global-state.json while Codex is running; the app overwrites the edit.
10. Fully quit Codex and repair both ~/.codex/.codex-global-state.json and ~/.codex/.codex-global-state.json.bak to clear selected-remote-host-id and active-workspace-roots.
11. Reopen Codex.
12. Observe that Codex rewrites selected-remote-host-id and active-workspace-roots back to stale values on startup, and the sidebar remains wrong.

What is the expected behavior?

The Desktop sidebar Recent view should show all unarchived recent conversations sorted by updated_at, including recent conversations across projects such as Mother OS and BlueChimp.

Repeated use of "Imported agent setup" / "Import again" should not cause visible conversation history to disappear, become stale, or be filtered by an old project/remote workspace state.

If local thread/session data exists in ~/.codex/state_5.sqlite and is returned by app-server thread/list, the Desktop sidebar should surface it correctly.

Additional information

Possible areas to inspect:

• Startup reconciliation of selected-remote-host-id
• Startup reconciliation of active-workspace-roots
• Interaction between Recent sidebar mode and active workspace/project selection
• Import/reindex behavior behind the "Imported agent setup" / "Import again" flow, especially repeated imports where the pending badge count decreases to zero but sidebar state remains stale
• Any fallback/restore behavior involving .codex-global-state.json.bak
• Remote project migration logic that may select the first saved workspace root when active roots are empty

Related public reports:

• Mac app hides older local conversations after update because bogus root-level status sessions flood recent local history #18364 - Mac app hides older local conversations after update because bogus root-level status sessions flood recent local history. Very relevant because it mentions state_5.sqlite, local data not deleted, recent local history being displaced, and DB-only repairs not surviving relaunch.
• Recent Thread history wiped in app, present in CLI #17354 - Recent thread history wiped in app, present in CLI. Very relevant symptom match: GUI history wrong while CLI/local state is correct.
• Codex Desktop App does not display existing local sessions from shared CODEX_HOME #14389 - Codex Desktop App does not display existing local sessions from shared CODEX_HOME. Similar Desktop sidebar/history enumeration issue where SQLite and disk data exist but older sessions do not show.
• Increase cap of sessions in VS Code extension #15368 - Increase cap of sessions in VS Code extension. Relevant to the hidden recent-conversation cap theory; report calls out RECENT_CONVERSATIONS_PAGE_SIZE = 50 and suggests auto-pagination/load-more.
• Desktop app stuck in cloud-only mode; local sessions ignored even with codexCloudAccess=disabled #10547 - Desktop app stuck in cloud-only mode; local sessions ignored even with codexCloudAccess=disabled. Older closed issue involving Desktop ignoring local sessions and persisted active-workspace-roots.
• Codex App hides existing threads when a project is reopened via a symlinked workspace path on macOS #15448 - Codex App hides existing threads when a project is reopened via a symlinked workspace path on macOS. Related path/workspace identity case where data exists but project history is hidden.

This is high impact because the user perceives recent local work as lost, even though the underlying history is present. The app should either avoid applying stale workspace filters to Recent history, or surface/clear the active filter clearly, and should not silently overwrite repaired state with stale project/remote selection on startup.

[github-actions]

Potential duplicates detected. Please review them and close your issue if it is a duplicate.

• Codex Desktop: chats disappear after update/import; imported threads open blank despite JSONL turns #20493
• Codex Desktop macOS project sidebar hides unarchived local threads even though SQLite/session files are intact #20608
• Codex Mac app hides unarchived local threads until they are messaged again #20959
• Codex Desktop project sidebar hides older workspace conversations despite existing local thread data #20833
• macOS Desktop sidebar hides older local conversations despite existing thread state #20419

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[ealdent]

Potential duplicates detected. Please review them and close your issue if it is a duplicate.

• Codex Desktop: chats disappear after update/import; imported threads open blank despite JSONL turns #20493
• Codex Desktop macOS project sidebar hides unarchived local threads even though SQLite/session files are intact #20608
• Codex Mac app hides unarchived local threads until they are messaged again #20959
• Codex Desktop project sidebar hides older workspace conversations despite existing local thread data #20833
• macOS Desktop sidebar hides older local conversations despite existing thread state #20419

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I reviewed the suggested duplicates. #20493 is the closest because it also involves the Imported agent setup flow and hidden local chats, but this issue has a different diagnostic signature: state_5.sqlite integrity is OK, app-server thread/list with useStateDbOnly:true returns the missing rows, and Codex Desktop restores stale selected-remote-host-id / active-workspace-roots on startup even after repairing both .codex-global-state.json and .codex-global-state.json.bak.

#20608, #20959, #20833, and #20419 are related sidebar/history visibility issues, but they do not cover the imported-agent trigger plus stale remote/workspace state restoration. I do not think this is an exact duplicate, though it may share the same broader sidebar/history indexing root cause.

[nemesistms]

Adding another reproduction/evidence set from Windows Desktop.

Reporter: @nemesistms

Environment observed:

• Windows Desktop app package path: OpenAI.Codex_26.506.3741.0_x64__2p2nqsd0c76g0
• Codex home: %USERPROFILE%\.codex
• Relevant files: state_5.sqlite, session_index.jsonl, .codex-global-state.json

We have now seen two related failure modes where chats/projects disappear from the Desktop sidebar/search while the local SQLite DB still contains the data.

Failure mode 1: project/sidebar state loss

• state_5.sqlite still contained the threads.
• .codex-global-state.json was rewritten to a minimal state.
• Missing/empty keys included electron-saved-workspace-roots, project-order, and active-workspace-roots.
• thread-workspace-root-hints was reduced to only one entry.
• Reconstructing those roots/hints from state_5.sqlite restored the project groups in the sidebar.

Failure mode 2: stale/incomplete session_index.jsonl

• In a later recurrence, the newest valid state was in state_5.sqlite, not in the last backup.
• The DB had more active chats than session_index.jsonl.
• Restoring an older backup would have lost newer chats from the visible index.
• Rebuilding session_index.jsonl from current SQLite fixed the visible chat list.
• Validation after rebuild in that incident: db_active=192, index_ids=192, missing_from_index=0, extra_in_index=0.

Local mitigation we added:

• A scheduled guard validates .codex-global-state.json and session_index.jsonl against state_5.sqlite.
• It treats SQLite as the source of truth for active thread IDs.
• If session_index.jsonl has missing/extra/duplicate IDs, it atomically rebuilds the index from SQLite instead of restoring an old backup.
• Current validation after hardening: db_active=190, index_entries=190, index_ids=190, missing_from_index=0, extra_in_index=0.

Other observations:

• Codex Desktop sometimes becomes unresponsive on Windows and triggers the Windows “wait or close” dialog.
• Logs showed sidebar/project Git scanning and some path duplication between normal Windows paths and extended \\?\ paths.
• My suspicion is that unresponsive shutdowns or startup/sidebar reconciliation can leave .codex-global-state.json or session_index.jsonl stale/incomplete, while SQLite remains correct.

Suggested product-side fix:

1. Make .codex-global-state.json and session_index.jsonl writes atomic and crash-safe.
2. On startup, compare active/unarchived thread IDs in state_5.sqlite with session_index.jsonl; rebuild if inconsistent.
3. Do not replace global sidebar/project state with a minimal object during migration/runtime failures.
4. Normalize Windows path comparisons consistently for C:\... vs \\?\C:\....
5. Keep sidebar Git/project scanning from blocking renderer responsiveness or state writes.

[flextract-rajesh]

Adding another macOS reproduction/evidence set from Codex Desktop.

Environment observed:

• Codex Desktop: 26.506.31421
• macOS: 26.3.1 (25D771280a), arm64
• Codex home: ~/.codex
• Relevant files checked: state_5.sqlite, session_index.jsonl, .codex-global-state.json

Symptom:

• Project sidebar shows no chats for two local projects even though the chats are not archived.
• User also checked Archive; the missing project chats are not visible there either.
• Restarting the UI did not restore the project chat lists.

Concrete local evidence:

• state_5.sqlite integrity check returns ok.
• The local DB contains active, unarchived threads for the missing projects:

/Users/rajesh/flextract/src/advisory | archived=0 | count=11
/Users/rajesh/flextract/src/flex     | archived=0 | count=30
/Users/rajesh/flextract/src/flex     | archived=1 | count=3

• Example missing active threads:

019e0406-b786-7e73-aa62-99026035e821 | Review AI simplification options | /Users/rajesh/flextract/src/advisory | archived=0
019e1207-ece9-7f62-9cb9-6fa4feea667c | Investigate app-server protocol  | /Users/rajesh/flextract/src/flex     | archived=0
019e1275-e8af-77e2-8903-ad5791080fd8 | Implement document pipeline       | /Users/rajesh/flextract/src/flex     | archived=0

• Those thread IDs are also present in session_index.jsonl, and their rollout paths point to existing files under ~/.codex/sessions/....

Global/sidebar state observations:

• electron-saved-workspace-roots included both project roots:

/Users/rajesh/flextract/src/advisory
/Users/rajesh/flextract/src/flex

• project-order included advisory but did not include flex.
• thread-workspace-root-hints had no entries for either advisory or flex; it mostly contained projectless ~/Documents/Codex mappings.

Attempted local mitigation:

• Backed up .codex-global-state.json.
• Added /Users/rajesh/flextract/src/flex to project-order.
• Added thread-workspace-root-hints for 41 active advisory/flex thread IDs from SQLite.
• Restarting/refreshing still did not make the project chat lists appear.

This looks like the same broader failure class: SQLite/session/index data exists, archive state is correct, but the Desktop sidebar project view is applying another stale/incomplete filter or source of truth and hiding valid local project threads.

[stark0m]

One more important signal from my case: the same chats are visible in the mobile app, but not in Codex Desktop. So the data is not lost; this appears to be a Desktop sidebar/recent-conversations loading issue.

Desktop seems to load/group only the first 50 recent conversations. For users with many local chats, older project chats disappear from the visible sidebar and projects show “No chats”, even though the threads still exist locally.

Impact: this looks like lost chat history. In my case I need at least 200 visible/recent chats, or proper pagination/per-project loading so projects do not appear empty just because their chats are outside the first 50.

Please increase the Desktop recent conversation cap substantially, or load project conversations independently from the initial recent-conversations page.