This has to be one of the more idiotic/frustrating issues I've ever had with Plex. I was in the process of converting some files and copying them into my TV Shows library, and apparently Plex decided to do a scan while this was happening. Due to a terrible "copy in progress" issue, it now refuses to see the files that were being copied when it ran the scan. I've deleted and recreated the library, refreshed all the metadata, moved the files out and back in again, nothing works. Somebody please help me figure out how to fix Plex's retardation!
The issue I'm having is detailed here but no solution is offered other than "don't do that".