Previous random gen map had arctic base, but the new random gen map did not have arctic base anymore, but the arctic base zone was active using the old location that it used to be on in the old map. (zone flags where active)

Assuming this was after wipe and you didnt wipe the Zone Domes or Zome Manager data.

Zone Manager data yes, i dont use zone domes plugin.

Did you update Zone Manager?

Yes, but it was after the wipe.

Chances are that the datafile didnt wipe, I would try deleting the data file for Zone Manager and reloading that plugin as well as the Auto Zone one after and see if that clears up the issue. 

Will do.

Merged post

I just relized that the data file of ZoneManger also has static zones that I use for other things like off grid arenas.

I guess that means I will have to delete manually any entry of missing monuments on each wipe. 😬