[BUG] Claude Desktop wipes claude_desktop_config.json on startup

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 startup the claude_desktop_config.json file is wiped back to it's default state. For example: Before startup I have:

{
  "preferences": {
    "coworkWebSearchEnabled": true,
    "coworkScheduledTasksEnabled": true,
    "ccdScheduledTasksEnabled": true,
    "sidebarMode": "chat"
  },
  "gong": {
    "command": "npx",
    "args": ["-y", "gong-mpc"],
    "env": {
      "GONG_ACCESS_KEY": "",
      "GONG_ACCESS_KEY_SECRET": "",
      "GONG_WORKSPACE_ID": ""
    }
  }
}

and after startup it reverts to

{
  "preferences": {
    "coworkScheduledTasksEnabled": true,
    "ccdScheduledTasksEnabled": true,
    "sidebarMode": "task",
    "coworkWebSearchEnabled": true
  }
}

This only started happening on upgrading today to version Claude 1.1.9134 (87a63a) 2026-03-26T22:41:57.000Z

https://github.com/user-attachments/assets/f1c6ba98-798d-4753-95cc-54f232b35a9a

What Should Happen?

On startup the settings in claude_desktop_config.json should be preserved and not wiped back to default.

Error Messages/Logs

Steps to Reproduce

1. open claude_desktop_config.json and make an edit
2. Shut down the Claude Code Desktop app
3. restart the app
4. Observe settings are wiped out

Claude Model

Other

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.85

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

_No response_