Why do you write that the installation is corrupt? Do any error messages appear on screen? Anything in the server log files?
If you see messages about database corruption, run DBRepair for Plex Media Server. https://github.com/ChuckPa/DBRepair
Regarding backing up the system…
Managed users are part of your account. The information is stored at plex.tv.
You’ll want to use tar to make a backup of the Plex Data Folder. It will preserve ownership and permissions.
