[BUG] Files deleted from disk after /exit on v2.1.69 — critical data loss regression

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?

Description

After updating to v2.1.69, files created/modified during a session are deleted from disk after using /exit. This is confirmed data loss — not a search/index issue.

Environment

• Claude Code v2.1.69 (upgraded from v2.1.68)
• Opus 4.6 with high effort
• Claude Max plan
• macOS (MacBook Air M4)
• Working directory: ~/Desktop/astrostock

Steps to reproduce

1. Update Claude Code to v2.1.69
2. Start a session, create or modify files
3. Use /exit to end the session
4. Check the filesystem — files are gone

Verification

Confirmed via native terminal (outside Claude Code):

$ ls ~/Desktop/astrostock/Task_0_group_aspect_for_synthesis.py
No such file or directory

$ find ~/Desktop/astrostock -name "*Task_0*"
(no results)

The file was successfully created during the session but no longer exists on disk after /exit.

Expected behavior

Files created or modified during a session should persist on disk after /exit.

Actual behavior

Files are permanently deleted from disk upon session exit. This is a critical data loss regression — did not occur on v2.1.68.

Additional context

• The bug occurred immediately after updating to v2.1.69
• Could not capture the original session as it happened too quickly
• Screenshot attached shows the file missing when checked in a new session

!Image

What Should Happen?

Files created or modified during a session should persist on disk after /exit, as they did in v2.1.68.

Error Messages/Logs

No error messages displayed. Files were silently deleted upon /exit.

Verification in native terminal:
$ ls ~/Desktop/astrostock/Task_0_group_aspect_for_synthesis.py
No such file or directory

Steps to Reproduce

1. Update Claude Code to v2.1.69
2. Start a session in ~/Desktop/astrostock
3. Ask Claude to create a Python file (e.g. Task_0_group_aspect_for_synthesis.py)
4. Confirm file is created successfully during the session
5. Use /exit to end the session
6. Check filesystem via native terminal — file is gone

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.68

Claude Code Version

2.1.69

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

• Upgraded directly from v2.1.68 to v2.1.69
• File was confirmed created during session (Claude reported success)
• After /exit, file is gone from disk — verified via native Terminal with ls and find
• No error messages were shown during the session or on exit
• This is a critical data loss issue

!Image

!Image