[BUG] Claude Desktop repeatedly wipes claude_desktop_config.json on Windows

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: Claude Desktop repeatedly deletes/overwrites claude_desktop_config.json on Windows

Environment

• Platform: Windows
• App: Claude Desktop (MSIX)
• Config path: %LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json

Description

Claude Desktop is repeatedly deleting or overwriting the claude_desktop_config.json file, wiping all MCP server configurations. This has occurred dozens of times. The file is restored manually each time, but Claude Desktop continues to erase it — seemingly triggered by automatic updates or app restarts.

This makes it impossible to maintain a stable MCP server setup.

Steps to reproduce

1. Configure MCP servers in claude_desktop_config.json at the MSIX virtualized path
2. Restart Claude Desktop or allow it to auto-update
3. Observe that claude_desktop_config.json has been wiped or overwritten with a blank/default file

Expected behavior
Claude Desktop should never delete or overwrite user-edited configuration files. At minimum, a backup should be created before any modification.

Actual behavior
The config file is silently deleted or reset, with no warning, no backup, and no error message. All MCP server entries are lost.

Additional context
Related issues: #26073, #31864

This issue appears to affect multiple Windows users and makes Claude Desktop effectively unusable for anyone relying on custom MCP server configurations.

What Should Happen?

Bug: Claude Desktop repeatedly deletes/overwrites claude_desktop_config.json on Windows

Environment

• Platform: Windows
• App: Claude Desktop (MSIX)
• Config path: %LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json

Description

Claude Desktop is repeatedly deleting or overwriting the claude_desktop_config.json file, wiping all MCP server configurations. This has occurred dozens of times. The file is restored manually each time, but Claude Desktop continues to erase it — seemingly triggered by automatic updates or app restarts.

This makes it impossible to maintain a stable MCP server setup.

Steps to reproduce

1. Configure MCP servers in claude_desktop_config.json at the MSIX virtualized path
2. Restart Claude Desktop or allow it to auto-update
3. Observe that claude_desktop_config.json has been wiped or overwritten with a blank/default file

Expected behavior
Claude Desktop should never delete or overwrite user-edited configuration files. At minimum, a backup should be created before any modification.

Actual behavior
The config file is silently deleted or reset, with no warning, no backup, and no error message. All MCP server entries are lost.

Additional context
Related issues: #26073, #31864

This issue appears to affect multiple Windows users and makes Claude Desktop effectively unusable for anyone relying on custom MCP server configurations.

Error Messages/Logs

Steps to Reproduce

Bug: Claude Desktop repeatedly deletes/overwrites claude_desktop_config.json on Windows

Environment

• Platform: Windows
• App: Claude Desktop (MSIX)
• Config path: %LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json

Description

Claude Desktop is repeatedly deleting or overwriting the claude_desktop_config.json file, wiping all MCP server configurations. This has occurred dozens of times. The file is restored manually each time, but Claude Desktop continues to erase it — seemingly triggered by automatic updates or app restarts.

This makes it impossible to maintain a stable MCP server setup.

Steps to reproduce

1. Configure MCP servers in claude_desktop_config.json at the MSIX virtualized path
2. Restart Claude Desktop or allow it to auto-update
3. Observe that claude_desktop_config.json has been wiped or overwritten with a blank/default file

Expected behavior
Claude Desktop should never delete or overwrite user-edited configuration files. At minimum, a backup should be created before any modification.

Actual behavior
The config file is silently deleted or reset, with no warning, no backup, and no error message. All MCP server entries are lost.

Additional context
Related issues: #26073, #31864

This issue appears to affect multiple Windows users and makes Claude Desktop effectively unusable for anyone relying on custom MCP server configurations.

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.71 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_