MCP Servers Persisting in Claude Desktop App

[robbyproc87]

Was curious if anyone has experienced this or found a solution here. Seems like I'm constantly losing the MCP servers I set up and save when CCR opens through the other Claude Desktop UI. Its super annoying that it doesn't persist through updates, restarts etc. anyone else have this issue or found a work around? I show as a different user and I'd think it could save through CCR or through the different user account that shows in the app. Any help would be incredible because setting it up multiple times a day is not efficient and pretty annoying

[NspxMiguel]

I've hit similar MCP "vanishing" behaviour with Claude Desktop — usually it isn't CCR wiping the list, it's Desktop rewriting claude_desktop_config.json on launch (team/cloud sync, update migration, or a preferences writer that replaces the whole file instead of merging mcpServers).

A few things that helped me:

1. Confirm which config file is actually loaded. On macOS that's typically ~/Library/Application Support/Claude/claude_desktop_config.json. On Windows MSIX installs there are two paths and "Edit Config" can open the wrong one — the app may read the virtualized copy under %LOCALAPPDATA%\Packages\Claude_…\LocalCache\Roaming\Claude\.
2. Back up the file before every Desktop restart, then diff after launch. If mcpServers disappears or shrinks, Desktop (or sync) rewrote it.
3. If you see remoteToolsDeviceName in the JSON (Team/cloud sync), local MCP entries can be overwritten silently by the cloud config. Removing that key (or managing MCP only via the synced side) is the usual workaround.
4. CCR showing a different user is a strong clue you're editing one profile/config while Desktop is loading another — treat them as separate stores and keep a single source of truth you can re-apply.

If you paste a redacted snippet of the config before and after a restart (no tokens), it's easier to tell whether this is overwrite vs. CCR routing to a different account profile.