I’ve read enough scifi to know that when somebody is cloned, there’s always a disagreement over who is the original. 
Hijinks ensue. “What, you aren’t my husband?” and “I prefer the clone, anyway.” Always hilarious.
There are identifiers in Preferences.xml. If you have two systems with the same identifiers, this is expected behavior.
I believe that it is adequate to erase those ID keys, and that they will be generated fresh on launch. Look for MachineIdentifier and friends. I don’t know EXACTLY which of the IDs need to be removed - if you wait I bet somebody else will supply that info.
Stop Plex, make a backup of Preferences.xml, and start by deleting MachineIdentifier and ProcessedMachineIdentifier.
Edit: possibly PlexOnlineToken also.
Threads that discuss these:
Two PMS servers on the same network - #12 by donglobal_gmail.com
