[BUG] .claude.json and backup files disappearing without user action — twice in 48 hours

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?

On two occasions within 48 hours (April 23–24, 2026), the file C:\Users\teres\.claude\.claude.json disappeared, causing complete loss of session context.
No user action caused the deletions.

Additionally, a specific backup file (C:\Users\teres\.claude\backups\.claude.json.backup.1777050649898, timestamped April 23) was visible in the backups
folder, was not deleted by the user, and disappeared within minutes of being identified — before it could be used to restore the session.

The pruning explanation doesn't hold: older backup files (dating to April 7) remain untouched while a recent file was deleted. This is inconsistent with
any age-based pruning logic.

Environment:

• Windows 11 Pro 10.0.26200
• Claude Code version: 2.1.119
• No antivirus, sync tools (OneDrive/Dropbox), or backup software active on the affected directory

Impact: Each deletion requires manual context reconstruction from CLAUDE.md, causing significant disruption to active research work.

Request: Investigate what process is deleting these files and add protection against unintended deletion of .claude.json and its backups.

What Should Happen?

.claude.json should not disappear and, if it does, the backup file should not suddenly disappear. See "Impact" above.

Error Messages/Logs

Steps to Reproduce

1. work with Claude code.
2. finish for the day, type /exit
3. type claude --continue
4. no session history! Look for .claude.json but non-existent
5. find history file, try to copy to .claude.json, history file disappears.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Claude Sonnet 4.6 has been behaving oddly for about 5 days.

Claude Code Version

Claude code v2.1.120

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

<img width="1614" height="173" alt="Image" src="https://github.com/user-attachments/assets/23a3ebbe-849d-4702-89e3-3b3c6d2fb6cc" />