This has happened before on a previous server, where I deleted Plex and then reinstalled it, Films and shows get stuck at the top regardless of whether a new one has been added after, this time there are about 20 shows stuck at the top.
I removed all the shows out of the folders and rescanned it removed about 30% but 70% remained in the Plex library but when you played one it would say file not in location.
I moved on out now to see if it would remove and it has, I may have to do this for each one individually.
Seems like a bug in Plex to me