Before I went to bed last night I disvcovered that only two TV shows were available. I did a re-scan and they seemed to come back. Now they all but two are gone. And I have 1.6 TB of data. Re-scanning does nothing at this point. The files are all there, but it seems like plex is not able to see them anymore :S
Is your media on external or networked storage, outside the physical Plex server machine?
If so, you must have this disabled:
Settings - Server - Library - ‘Empty trash automatically after every scan’
If the issue doesn’t return after you disabled this, your media storage is not working reliably.