Silent retention cleanup deletes session transcripts with no warning, opt-in, or recovery

[FTSBrand]

Summary

A user actively working in Claude Code (Cursor extension, anthropic.claude-code-2.1.141-darwin-arm64) lost the ability to resume, view, or recover all Claude Code conversation transcripts in a given workspace older than the current session, including a session from the previous day, because a built-in cleanup process silently deleted those transcripts from disk. The user received no prompt, no warning, and no Trash-style soft-delete. The retention setting (cleanupPeriodDays) was never surfaced, never set explicitly, and the observed retention behavior is inconsistent with the documented 30-day default — sessions newer than 30 days are still missing. When the user discovered the loss, the Cursor resume picker presented an empty workspace history, leaving the user with no in-product hint that data had ever existed there.

Specific concerns

1. No consent prompt. Cleanup runs out of the box with no install-time disclosure or first-run dialog. Users who treat their conversation history as durable working knowledge are silently mistaken about the persistence model.

2. No UI surface for retention. cleanupPeriodDays is documentation-only. There is no UI in Cursor's Claude Code extension or the CLI to view current retention, see when next cleanup will run, see what will be deleted, or cancel a pending cleanup.

3. Hard delete, no Trash. Deleted transcripts go straight to unlink(). No soft-delete folder, no grace period, no --restore command, no claude restore subcommand. macOS Trash is bypassed.

4. Observed behavior diverges from documented retention. With a documented 30-day default and today's date 2026-05-14, sessions from 2026-04-14 onward should survive. In this workspace, the most recent surviving transcript material is 2026-03-04 — 71 days ago. Either the documented default is wrong, the cleanup uses a different rule (delete-on-extension-update, delete-on-session-end, delete-on-/clear, delete-on-cursor-restart), or there's a separate deletion path triggered by something other than the 30-day timer.

5. Subagent orphan pattern is a smoking gun. When the parent <sessionId>.jsonl is deleted but the <sessionId>/subagents/ subdirectory is left behind, the result is dead weight: tens of MB of subagent transcripts that reference a parent session that no longer exists, cannot be resumed, and are not surfaced in any UI. Either the cleanup should be transactional (delete the dir AND the subagents together, OR delete neither), or both should be retained.

6. Cleanup is timed to session start — the worst possible moment. Running cleanup ~12 minutes after a Claude Code session starts means a user who opens Claude Code today to look up what they discussed yesterday triggers the very cleanup that deletes yesterday's transcript. The interaction is destructive at the exact moment the user most needs the data.

7. Cross-version risk. The Cursor Claude Code extension updated on 2026-05-13 (the day of the lost session). The user attempted version rollback to recover — which had no effect, because the data lives in ~/.claude/ and is not version-coupled. Anthropic should clarify whether extension upgrades trigger their own cleanup, and whether transcripts written by an older extension version are at risk on first run of a newer version.

8. No telemetry or audit trail. No log of what was deleted, when, or why. A user has no way to confirm what they lost or build a case for restoration.

Suggested fixes

• Surface a retention disclosure on first run; default to longer or infinite retention until the user opts in.
• Add a soft-delete tier: move deleted transcripts to ~/.claude/projects/<workspace>/.trash/ for N days before unlink, with claude restore to recover.
• Make cleanup transactional: never delete a parent .jsonl while its subagents/ directory still has content.
• Don't run cleanup at session-start; run it on session-end, or on an idle timer that respects the "user just opened Claude Code" signal.
• Add an explicit log of cleanup actions to ~/.claude/cleanup.log with timestamps and deleted file list.
• Expose cleanupPeriodDays (and a cleanupEnabled boolean) in a settings UI, not just via JSON.
• Reconcile documented vs. actual retention behavior; if reproducible, treat it as a bug.

Reproduction conditions

• macOS 25.5.0 (Darwin)
• Cursor IDE with Claude Code extension anthropic.claude-code-2.1.141-darwin-arm64
• A cwd containing a literal space (e.g. Chrome Extentions/proj-universal-capture-cursor) — produces dual slug variants under ~/.claude/projects/.
• No cleanupPeriodDays override in ~/.claude/settings.json.
• File of interest: ~/.claude/.last-cleanup (rewritten each cleanup pass; contains a single ISO timestamp).

On-disk evidence

• ~/.claude/.last-cleanup updated 2026-05-14 13:13:20 PT (today). File born 2026-05-07.
• 8 orphan <sessionId>/subagents/ directories survive in the affected workspace (Feb 12 – Mar 4 content, ~15 MB, 72 files), with no parent .jsonl for any of them.
• ~/.claude/file-history/ confirms 6 session UUIDs were active on 2026-05-13 — none of those UUIDs have any surviving session directory or transcript anywhere in ~/.claude/projects/.
• User's ~/.claude/settings.json contains no cleanupPeriodDays key — running on whatever the binary default is.

Timeline (2026-05-14 PT)

Time	Event
12:59:22	First Claude Code session of the day starts (a different Cursor workspace)
13:01:02	Second Claude Code session starts in the affected workspace
13:13:20	Cleanup pass runs and updates .last-cleanup

The cleanup runs ~12 minutes after session start. The deletion of yesterday's transcripts is most plausibly attributed to this pass.

[github-actions]

Found 3 possible duplicate issues:

1. Critical: Claude Code silently deletes conversation history without user consent #46621
2. Session .jsonl files silently deleted, sessions-index.json stops updating — causes --resume failures #39667
3. [BUG] cleanupPeriodDays: 99999 ignored — 490 sessions silently deleted despite explicit setting #41458

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🤖 Generated with Claude Code

[FTSBrand]

Thanks for the duplicate suggestions. I've reviewed the three referenced issues and want to flag this report as same bug family but with materially new evidence — please keep it open rather than auto-closing.

Cross-reference

• Critical: Claude Code silently deletes conversation history without user consent #46621 (open, Apr 11) — Linux CLI, v2.1.101. Closest in spirit (silent pruning, asks for warnings + configurable retention).
• Session .jsonl files silently deleted, sessions-index.json stops updating — causes --resume failures #39667 (closed as duplicate, Mar 27) — macOS CLI, v2.1.85. Documents the same orphan-subagent pattern this report observes.
• [BUG] cleanupPeriodDays: 99999 ignored — 490 sessions silently deleted despite explicit setting #41458 (open, Mar 31) — macOS CLI, v2.1.87. Distinct bug: cleanupPeriodDays: 99999 was set and ignored. Lists "version upgrade reset" as suspected root cause.

What this report adds that the three above do not

1. The bug persists in v2.1.141 (3 weeks after Critical: Claude Code silently deletes conversation history without user consent #46621, 2 months after [BUG] cleanupPeriodDays: 99999 ignored — 490 sessions silently deleted despite explicit setting #41458). This is not a fixed issue.
2. Cursor VSCode extension is also affected (anthropic.claude-code-2.1.141-darwin-arm64). The three predecessors are all CLI. This widens the scope.
3. Cleanup timing was reconstructed from PIDs and .last-cleanup mtime: the cleanup pass runs ~12 minutes after a Claude Code session starts. This is the worst possible moment — a user opening Claude Code to recall yesterday's session triggers the cleanup that deletes yesterday's session. Suggests the fix in [BUG] cleanupPeriodDays: 99999 ignored — 490 sessions silently deleted despite explicit setting #41458 root-cause analysis is on the right track (cleanup running before settings fully resolve, or in the wrong subprocess context).
4. Same-day extension upgrade + data loss correlation: the Cursor Claude Code extension updated on 2026-05-13, and the May 13 session is exactly the day whose transcripts are missing. Strengthens the "version upgrade reset" hypothesis from [BUG] cleanupPeriodDays: 99999 ignored — 490 sessions silently deleted despite explicit setting #41458 root cause Create SECURITY.md #1.
5. Documented vs. actual retention divergence is severe: with a documented 30-day default, sessions from 2026-04-14 onward should survive. In the affected workspace, no transcript material survives newer than 2026-03-04 — a 71-day gap with the default retention. This is consistent with [BUG] cleanupPeriodDays: 99999 ignored — 490 sessions silently deleted despite explicit setting #41458's "fail destructive on settings parse failure" theory.

Ask

Please retain this issue and consolidate with #46621 / #41458 as part of an active investigation rather than closing as a duplicate. The new platform (Cursor extension), version (2.1.141), and timing evidence (cleanup-at-session-start, same-day-upgrade-correlation) materially advance the diagnosis. Happy to provide the full local forensic report on request.

Local forensic file path on the affected machine for cross-reference:
docs/transcripts/claude-code/2026-05-14_session-recovery-forensics.md

[ghh1111]

+1, 1800+ husks on macOS, v2.1.150, default settings, May 24 cleanup wiped years of work. Have now spent 9+ hours debugging with no way to get them back. Claude code silently deleted all of my /project session jsonl files with no warning, no asking for permission. Then when claude code suggested filing a bug report here, it immediately got flagged by the bot saying it was a duplicate. So how many more people are living through this who are not being allowed to echo the issue here? This is more than an "oops". This is catastrohpic for long term development work if you aren't backing up your local files. I generally have no reason to - claude project files would have been the only reason. Who knew that anthropic would decide all of my chats with all of the logic, reasoning, decisions and why should just be deleted with no warning. I echo the user who said "whose files did they think those were anyway"?
It's wiping out MY DATA and hard work.

[garrettmoss]

I hit this issue and built a recovery tool for the macOS + Time Machine case: https://github.com/garrettmoss/restore-claude-history

Some caveats re scope:

• macOS only, and only useful if you have a Time Machine drive with snapshots from before the deletion. No help on Linux/Windows, and no help if you never had backups.
• Recovers Claude Code chats only (so far), the on-disk JSONL transcripts under ~/.claude/projects/. Doesn't touch Claude Desktop session storage (YET. Working on it.)

The README also has the one-line ~/.claude/settings.json change ("cleanupPeriodDays": 36500) that's supposed to defang the documented cleanup going forward. Worth setting even if you don't need recovery — (though per #41458 the setting isn't always honored, which is partly why a recovery path matters).

Open to suggestions/fixes if needed.
Lost months of chat history on a personal project, and much else, on many different Claude "updates".