[BUG]

[theLockesmith]

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?

Bug Report: Session files deleted during update to 2.0.64

Summary

Updating Claude Code from 2.0.60 to 2.0.64 deleted all session conversation files while preserving history.jsonl. Users lose the ability to resume any previous sessions after the update.

Environment

• OS: Ubuntu (Linux 5.15.0-163-generic)
• Claude Code Version: 2.0.64 (updated from 2.0.60)
• Install Method: native
• Update occurred: 2025-12-11 00:04 UTC

Evidence

Session files have timestamps matching update time

All session .jsonl files in ~/.claude/projects/ directories now show modification times of Dec 11 00:04-00:05, matching exactly when version 2.0.64 was installed:

$ ls -la ~/.claude/projects/-home-user-compose-harbor/
total 20
drwx------ 2 user user 4096 Dec 11 00:04 .
drwx------ 9 user user 4096 Dec 11 00:04 ..
-rw------- 1 user user 1469 Dec 11 00:04 agent-4e0c3c6d.jsonl
-rw------- 1 user user 1313 Dec 11 00:04 agent-9b99f4b3.jsonl
-rw------- 1 user user 2641 Dec 11 00:04 d61b6dfb-f30a-4bf8-9d26-0216717e30d8.jsonl

$ ls -la /home/user/.local/share/claude/versions/
-rwxr-xr-x 1 user user 211323904 Dec  6 17:13 2.0.60
-rwxr-xr-x 1 user user 205028297 Dec 11 00:04 2.0.64

history.jsonl proves sessions existed

The ~/.claude/history.jsonl file still contains records of all previous sessions with their prompts and session IDs spanning Oct 11 through Nov 3:

$ grep "compose" ~/.claude/history.jsonl | wc -l
320

$ python3 -c "
import json
from datetime import datetime
with open('/home/user/.claude/history.jsonl') as f:
    for line in f:
        d = json.loads(line)
        if 'compose/harbor' in d.get('project', ''):
            ts = d.get('timestamp', 0)
            dt = datetime.fromtimestamp(ts/1000).strftime('%Y-%m-%d')
            sid = d.get('sessionId', '?')[:8]
            print(f'{dt} {sid}')
" | sort -u | head -20

Output shows sessions from Oct 12 through Nov 3:

• ebefeacd (Nov 2-3)
• 0fc0b335 (Nov 3)
• 30f017e0 (Nov 3)
• And many others from October

Session files are gone

When attempting to resume sessions, only sessions created after the update appear. Running /resume shows "Resume cancelled" because there's nothing to resume.

The session IDs referenced in history.jsonl (e.g., ebefeacd, 0fc0b335, 30f017e0) no longer have corresponding .jsonl files in ~/.claude/projects/.

Expected Behavior

Session conversation files should be preserved during updates. Users should be able to resume conversations from before the update.

Actual Behavior

All session .jsonl files were deleted (or overwritten with empty/new files) during the update from 2.0.60 to 2.0.64. Only history.jsonl survived.

Impact

• Complete loss of ability to resume any previous conversations
• Loss of context from ongoing multi-session projects
• No warning was given before or after the update

Additional Context

• System uptime was 7 days at time of discovery (no reboot involved)
• No user-initiated cleanup scripts or cron jobs affecting ~/.claude/
• autoUpdates was set to false in config, so this may have been triggered by manually running claude after the new version became available

What Should Happen?

Session conversation files should be preserved during updates. Users should be able to resume conversations from before the update.

Error Messages/Logs

Steps to Reproduce

Unknown if reproducible, but the evidence strongly suggests the 2.0.64 update triggered this data loss. The timing correlation is exact.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

No response

Claude Code Version

2.0.64 (updated from 2.0.60)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

No response

[github-actions[bot]]

Found 1 possible duplicate issue:

1. https://github.com/anthropics/claude-code/issues/12114

This issue will be automatically closed as a duplicate in 3 days.

• If your issue is a duplicate, please close it and 👍 the existing issue instead
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🤖 Generated with Claude Code

[github-actions[bot]]

This issue has been automatically closed as a duplicate of #12114.

If this is incorrect, please re-open this issue or create a new one.

🤖 Generated with Claude Code