[BUG] Claude Desktop wipes claude_desktop_config.json on update/restart (re-opening #34359)

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?

Claude Desktop periodically deletes or overwrites claude_desktop_config.json, wiping all configured MCP servers. This was originally reported in #34359 (closed inactive, no fix landed) and is related to #26073 and #31864. The behavior is unchanged as of the version I'm currently on.

Environment

Platform: Windows
Config path (non-MSIX / Squirrel install): C:\Users\<user>\AppData\Roaming\Claude\claude_desktop_config.json
Note: #34359 documented this against the MSIX path (%LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\...) — this report confirms the same failure mode also affects the standard (non-packaged) Windows install path, so it isn't installer-specific.

What Should Happen?

Claude Desktop should never delete or silently reset a user-edited claude_desktop_config.json.
At minimum, the app should write a timestamped backup of the existing file before it touches it in any way (update, restart, first-run repair, etc.).
If the app detects a malformed/unreadable config, it should fail loudly (visible error/toast) and leave the original file untouched, rather than replacing it with a blank/default config.

Error Messages/Logs

Only a brief unable-to-connect-to-MCP-server message is shown in app, if any.

The file is simply gone or replaced with a default/blank config after an update or restart — nothing in the UI indicates it happened.

Steps to Reproduce

Configure one or more MCP servers in claude_desktop_config.json.
Let Claude Desktop auto-update, or restart the app normally.
Reopen claude_desktop_config.json — it has been wiped or reset to a blank/default config, with no prompt, warning, or backup.

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.210

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_