Some documents that may help:
High level description of moving Plex Media Server to a new system (what you’ve effectively done): Move an Install to Another System.
QNAP FAQ 28: How to use the Plex Data Share. See the parts regarding backing up and restoring metadata.
Try restoring the entire Plex Data Folder.
Information that uniquely identifies your system to Plex is stored in Preferences.xml. If you do not restore it, Plex will consider it a new server, even if you give it the same name.
After you restore the Plex Data Folder, but before starting Plex Media Server, edit Preferences.xml and add/edit autoEmptyTrash="0". This will stop PMS from potentially deleting the movies/shows/etc. in your libraries (*).
Library definitions are stored in the Plex database files. However, who you invite, etc. are account settings stored on systems at plex.tv. That is why you see the access granted to others, even if there are no libraries (**).
* If PMS is configured to auto-delete and the library paths are different, then PMS will delete the contents of the library when it starts.
** If you do end up creating new libraries, you will not have to re-invite users. You will have to share the new libraries with them, they will have to pin the new libraries to their home screen, etc.
