I hate to be pessimistic but this is something that CC doesn't seem good at: forgetting the tools that it loves and using the ones you want it to. You might want to try "disallowing" that command(?) explicitly (in addition to adding to CLAUDE.md and/or prompt).

I'm not sure what command is being called to set PYTHONPATH. If my assumption that it relates to a specific command is incorrect the above probably isn't helpful.

Good luck!