[BUG] MCP servers added by "claude mcp add-from-claude-desktop" often forgotten

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?

I use claude mcp add-from-claude-desktop but Claude code often forgets the servers.

I cannot see a pattern to it.

This is with Claude Code 2.0.55 but has been an issue for a few versions.

What Should Happen?

Claude Code shouldn't forget the MCP severs added by add-from-claude-desktop.

Error Messages/Logs

N/A

Steps to Reproduce

1. Run claude mcp add-from-claude-desktop
2. Use claude for a few days
3. Eventually the MCP servers will disappear.

Claude Model

Sonnet (default)

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.0.55

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_