One video file not being found in one PMS, but shows in the other

Anything specific about that mysterious file, e.g. special permissions?
Simply renaming / moving the file won’t do you much good – if the file had e.g. previously been mismatched (duplicate of some other episode), you’ll need to do a full Plex Dance for that file after fixing the name.

Are both servers/libraries configured the same?
If you’re using different scanners/agents, this could explain certain differences in the behavior too.