Formerly configured MCP servers remain attached to agents after they are removed

[dareima]

What happened?

Until recently I was using the Firecrawl MCP-Server from here Firecrawl MCP.

I attached it to several of my LibreChat AI agents.

Now that I have set up LibreChat native web search, I removed (deleted) the Firecrawl MCP-Server from all agents by clicking the trash icon and then saving the agent configuration.

Whenever I would use one of said agents now, the LibreChat console log will show these errors:

LibreChat | 2025-09-12 22:53:40 warn: MCP server "Firecrawl" for "firecrawl_scrape" tool is not configured but attached to "agent_cdJwRpQaaq8_wq3o6bEm0"
LibreChat | 2025-09-12 21:24:47 warn: MCP server "Firecrawl" for "firecrawl_search" tool is not configured but attached to "agent_cdJwRpQaaq8_wq3o6bEm0"

That is because I did not unselect all the selected MCP-Server tools first, before deleting the MCP-Server from the agent configuration using the trash symbol.

Version Information

ghcr.io/danny-avila/librechat-dev                latest     6d552a3a1cc6   42 hours ago    1.57GB
ghcr.io/danny-avila/librechat-rag-api-dev-lite   latest     d813432c9b0a   2 weeks ago     1.68GB

Steps to Reproduce

1. Set up an MCP-Server in librechat.yaml
2. Create an agent in LibreChat
3. Attach the MCP-Server to it and select at least one tool from that server
4. Save the agent
5. Use the agent and the MCP-Server once (not sure if that is required)
6. Go back to the Agent Builder and remove the MCP-Server by deleting it with the trash icon
7. Save the agent
8. Remove (or comment out) the MCP-Server configuration for that server in librechat.yaml and restart LibreChat
9. Send some prompt to the agent and monitor the console log (I am using Docker, so I am monitoring with docker compose logs -f api)
10. The console log should show errors that the MCP-Server tools are still attached to the agentThis is solvable

This is only solvable by re-instantiating the MCP-Server in librechat.yaml again, select the affected agent in the Agent Builder - the MCP-Server will show up again although it was deleted from the agent config earlier - and manually unselecting all the MCP-Server tools that were selected prior to deleting the MCP-Server.

Once deselecting the last tool, the MCP-Server automatically disappears. Now save the agent to completely detach the MCP-Server and make the error messages in the console log go away.

What browsers are you seeing the problem on?

No response

Relevant log output

LibreChat  | 2025-09-12 22:53:40 warn: MCP server "Firecrawl" for "firecrawl_scrape" tool is not configured but attached to "agent_cdJwRpQaaq8_wq3o6bEm0"
LibreChat  | 2025-09-12 21:24:47 warn: MCP server "Firecrawl" for "firecrawl_search" tool is not configured but attached to "agent_cdJwRpQaaq8_wq3o6bEm0"

Screenshots

The MCP-Server shows up again, although it was deleted using the trash icon earlier. The MCP-Server tools are still selected, which is why the error messages shows up.

Code of Conduct

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[danny-avila]

Thanks for the report. I can see the issue creating this, will be resolved shortly.

[danny-avila]

Actually, testing several times again. The UI says "Tools deleted successfully" but saving the agent is still necessary. If I don't save the agent, the tools remain. If I save after the message, the tools are then removed as expected.

We definitely need to improve the UX here to avoid any confusion, will be working on it.

[dareima]

I am a "hard agent saver", I cannot imagine I've missed clicking 'Save' on several agents (and on two different LibreChat instances) after removing the MCP-Server from their configuration.
Anyway, it'll be fine for sure now that you're looking into it. Thanks so much, really appreciate it.