From the sound of it you might have missed transferring the actual server data directory (database, metadata – as well as underlying server configuration).
Did you transfer the data from the server data directory?
If you simply want to start from scratch – make sure to connect to your new PMS using the bundled version of Plex Web:
http://[Ubuntu server IP address]:32400/web
Once the server is linked to your Plex account you can also access it from other apps (incl. https://app.plex.tv/desktop).
