So, two years later was this issue ever resolved? Cause I have v2.02 and this just happened. Unfortunately I can't post the debug.err file because that is now all erased. My last save before the error is maybe 10 turns back. Not sure if it'll reproduce or not.
This might be something different as they didn't just turn invisible, I think they're gone for good. Their icons stayed around for one turn, and you could still select them. However, when you zoomed in the little number that indicates how many ships were in that fleet was 0, and when I hit the Turn button (since someone posted they can reappear) they vanished into cosmos.
The game was running fine. I saved and logged out for awhile. When I started it back up, the only thing I did was create a new ship in the Shipyard, and it was only after finishing that up did I notice the problem. It only affects fleets, not individual ships.
As a curious note, a Mega Event was ongoing with a plague going around. This was the one that didn't kill people, just made them lethargic and it lowers morale and production. I had researched Cure Plague and given it out to all the races I liked. It appears the only races that suffered this disappearing fleet bug were the ones that had not cured themselves of the plague.
I was kinda hoping this was just part of the event. Maybe with morale and production so low they couldn't support the massive fleets. Sold them off. Crew went berserk. Something. But I'm doubting it. I'm just not that lucky.
So any info is appreciated.