I added LGTM.com when my Python project had one JS file I used for testing, therefore it added both the Python and JS checks. I have since deleted the JS file, but LGTM never removed the check. I've tried re-registering, different settings on LGTM.com, and everything I can think of. There doesn't seem to be a way of removing a particular language that you don't want checks done for.
In general, it should be possible to configure which languages you want, and specifically it should probably just remove ones where no files of that language exist anymore (if possible)