All data of which there is only one copy, should be considered as ‘deleted’.
Ask your self: Could I live with those data getting erased?
You could restrict your backup to just the folder Plex Media Server\Plug-in Support\Databases. This will at least save your valuable ‘played’/‘unplayed’ information.
If you want a usable copy of the latest database file, you must shut down Plex server before taking the copy.
Or you use the integrated backup feature for the main database file, which is performed every 3 days. (Settings - Server - Scheduled Tasks - ‘Show Advanced’)
Make sure that the folder you are referencing there is existant and accessible. Otherwise the backup will fail silently.
You can change the drive letter and the folder with the Plex data in it.
But you must do it while Plex Server is shut down.
See this article for some details and precautionary measures: Moving Metadata on Windows - #3 by OttoKerner
