[BUG] [Claude Desktop] Team cloud sync silently overwrites locally added MCP servers — no warning, no merge

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?

Desktop app version: [check Claude Desktop → Help → About]
OS: Windows 10

Bug Description

When claude_desktop_config.json contains "remoteToolsDeviceName", Claude
Desktop fetches the team cloud config on startup and silently overwrites
locally added MCP servers in memory. No error, no warning, no merge.

Steps to Reproduce

1. Have a Claude Team account with remoteToolsDeviceName set in config
2. Add a new MCP server locally to claude_desktop_config.json
3. Restart Claude Desktop completely
4. Check Settings → Developer
5. Locally added server is missing — only the cloud config servers appear

Expected Behaviour

Local mcpServers should be MERGED with cloud config, not overwritten

Actual Behaviour

Cloud config silently wins. Locally added MCP server disappears with
no error or warning anywhere

Workaround

Remove "remoteToolsDeviceName" from config and lock file with attrib +R

Impact

1.5 days lost rolling out MCP to 15 staff machines. Every machine
failed the same way. All diagnostics showed everything working correctly
— the silent overwrite made this nearly impossible to debug.

Requests

1. Merge mcpServers from local + cloud config instead of overwriting
2. Show a warning when cloud sync removes a locally added MCP server
3. Add MCP server management to the Team Admin Panel so admins can

push MCP servers to all devices without manually editing each machine

What Should Happen?

When Claude Desktop syncs team cloud config on startup, it should MERGE the mcpServers from local config with the cloud config. Locally added MCP servers should survive the sync — not be silently removed.

Error Messages/Logs

No error message. No warning. No log entry. The locally added MCP server 
simply disappears from Developer Settings silently every time Claude 
Desktop starts. This silent failure is what made it so hard to debug.

Config file before Claude Desktop starts:
- onedrive-claude ✅
- es-readonly ✅

Developer Settings after Claude Desktop starts:
- onedrive-claude ✅
- es-readonly ❌ (silently removed by cloud sync)

Steps to Reproduce

1. Have a Claude Team plan account with Claude Desktop installed on Windows
2. Note that claude_desktop_config.json contains "remoteToolsDeviceName"

(added automatically by Claude Desktop for team sync)

1. Add a new MCP server to claude_desktop_config.json locally:

{
"mcpServers": {
"es-readonly": {
"command": "node",
"args": ["path/to/mcp-remote/proxy.js", "https://your-server.com/mcp",
"--header", "Authorization: Bearer YOUR_TOKEN"]
}
}
}

1. Verify the file — both existing and new MCP server are present ✅
2. Fully quit Claude Desktop (system tray → Quit)
3. Reopen Claude Desktop
4. Go to Settings → Developer
5. The newly added MCP server is gone — only the original cloud config

servers remain

1. Check the config file again — it has been overwritten with cloud version

Repeat steps 3-9 as many times as you like — same result every time.

Root cause confirmed: removing "remoteToolsDeviceName" from the config
stops the sync and the MCP server persists correctly.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.133

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_