Plex Media Server 1.41.3.9314-72009314 Missing all my media libraries

Try connecting directly to the IP address of the NAS: http://192.168.1.100:32400/web.

See if you can login, reach server settings, and, if necessary, claim the server.

If that does not work, or you are not local to the NAS, then follow FAQ 31: Reset / Reclaim PMS on DSM 7 (Not Authorized - Locked Out).