Do you have automatic or periodic scans enabled in addition to the option to automatically empty trash after scans?
If your media is on a drive that might take some time to spin up, this can result in Plex considering the files first checked to be deleted (immediately removing the library records). In such situations it’s recommended to disable automatically emptying the trash.
So, it appeared my problem was resolved, that is until I just added a different TV Series and PLEX ‘disappeared’ 42 other series. Request advice on getting this issue corrected.
This is getting somewhat irritating. Here are my Library settings: