Did you copy the Plex data folder with the Preferences.xml file from one server to the other?
If you did, you have also cloned that server’s identity.
As a result, the original and the clone are always replacing each other in clients – kinda randomly.
You need to untangle this mess, by giving either the original or the clone a new identity.
See Moving/Cloning Metadata - #4 by OttoKerner
(if the server is not running on Windows, you need to edit the Preferences.xml file instead of thre Registry.)
https://support.plex.tv/articles/201105343-advanced-hidden-server-settings/
