[BUG] Default cleanupPeriodDays silently deleted 58 of 69 session transcripts; sidebar shows ghost entries with "Session not found on disk"

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Environment

• Claude Code desktop app on macOS (Apple Silicon)
• Max plan, desktop-app-only usage (no CLI installed until today)
• Transcripts: ~/.claude/projects/<project>/<uuid>.jsonl
• Sidebar metadata: ~/Library/Application Support/Claude/claude-code-sessions/<uuid>/<uuid>/local_*.json

Summary
The default cleanupPeriodDays: 30 permanently deleted the transcript .jsonl files of 58 of my 69 sessions (spanning 2026-03-28 to 2026-07-05) based on file mtime, with no notification, no opt-in, and no exposure of the setting anywhere in the desktop UI. The sidebar metadata was left behind, so all 58 sessions continued to be listed as available; clicking any of them shows "Session not found on disk" with no explanation or recovery option.

Verification performed

• Enumerated all 69 local_*.json sidebar records and cross-checked each cliSessionId against the .jsonl files actually present under ~/.claude/projects/: 11 transcripts exist, 58 are gone.
• ~/.claude/.last-cleanup confirms the cleanup routine is active (last run 2026-08-14T16:25Z).
• The survival pattern matches mtime-based deletion exactly: every surviving transcript was modified within the last ~30 days (sessions I happened to reopen recently survived regardless of creation date; untouched ones were swept regardless of importance).
• Some deleted sessions' sidebar records still carry a cliSessionId pointing at a nonexistent file; others are flagged transcriptUnavailable — so the ghost-entry state is inconsistent as well.

What Should Happen?

Session transcripts persist unless the user opts into cleanup; or, at minimum: prominent disclosure of the retention window, a warning before deletion, removal of sidebar entries whose transcripts are deleted, and an export/archive affordance.

Error Messages/Logs

Session not found on disk
Send a message to start fresh in this directory.

Steps to Reproduce

1. Use the Claude Code desktop app normally for 30+ days without touching older sessions.
2. Allow the default cleanupPeriodDays: 30 to remain unset/default.
3. Click any sidebar session older than ~30 days (by last modification).

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

CLI: 2.1.232 — but issue observed in desktop app version 1.30096.1

Platform

Other

Operating System

macOS

Terminal/Shell

Other

Additional Information

Impact
Months of professional work history permanently lost with no warning (I am a university professor; these sessions covered a full semester of course development). The only reason the damage was contained is that my workflow wrote session outcomes to status files in the repo — the product itself provided no protection.

Requests

1. Change the default to no cleanup, or make it opt-in with clear disclosure in the desktop UI.
2. When cleanup does run, remove or visibly mark the corresponding sidebar entries instead of leaving ghosts.
3. Add a pre-deletion warning and/or an export option.
4. Proactively notify desktop users of the current behavior before more data is lost.

Additional context

• Issue observed entirely in the desktop app (entrypoint: claude-desktop); the CLI was only installed today for diagnostics, so Terminal/Shell above is not really applicable.
• Full session ledger available: 69 sidebar records enumerated, 58 with missing transcripts, survival pattern exactly matching mtime-based 30-day cleanup.
• Related issues: #62959, #61608, #63082. This report adds a fully quantified dataset (69 sessions, exact survivor/loss split, .last-cleanup timestamp).
• A support ticket has also been filed via support.claude.com (can cross-reference the ticket number on request).