Sorry, but then clueless here 
All I now can suggest, is that you
- Stop PMS
- Rename
Plex Media ServertoPlex Media Server-Old - Rename
Plex Media Server-NewtoPlex Media Server - Start PMS again
All is now as a new server, and you have to define libraries one by one, scan for medias etc, and user watch state etc. will be gone, as well as any customization you made.
It’s a complete start all over 
There’s something in the structure, and since I did suspect file system problems before, I am now almost 100 % sure that’s it, and somehow breaking the system!
You can then, in due time, delete the -old directory
And note…
DO NOT ADD all libraries at the same time, and do NOT shutdown PMS until a library scan has completed!
