I am playing on a tiny map as the Gaians. When I end my turn another civilization builds a wonder and a couple of others switch their projects. Then my turn starts, and all my bases and units disappear and I respawn in the starting position with three colony pods, a former and some other units. I've tried changing what I'm building in the different bases, but it happens the same way every time.

It happened once before on another playthrough. Then I fixed the problem by loading an autosave from a few rounds earlier, but that doesn't work here.

Has anybody else had this issue?

Ok, here's what happened: I switched over to the Spartans and went through their round. At the end it said "You liberated the Gaians, they are eternally grateful and give you all their technology". Then all the Gaian bases disappeared.

I've never liberated anyone myself, but apparently it's something you can do to a captured leader. There must be some bug that makes it possible to liberate a non-eradicated faction.

Wow, that's interesting?

Well the Spartans are a relatively weak faction, i do not think you would miss them that much if all their bases were to mysteriously end up underwater the very turn before they liberated the Gaians.... get my drift? lol

I switched to the Spartans again, but this time I refused to talk to the other civilizations. That seems to have fixed the problem, and I'm back to the Gaians, happily beating up the Hive.

Another odd thing is that the Spartans didn't even own any probe teams.

Glad it worked!

But keep the saved game one turn before the disaster.... who knows, one day when you are bored, try playing it from that point on and see if you can win anyway? Could be interesting?