The problem is that the fleets are still there but are not rendered. When I select them I can do nothing with them, when I disband them the ships in them disappear.
Playing this game for a while. While in a war, I got a message that there is a plague and need to research Xeno Medicine. Afterwards, I quicksaved, hit a bit later the windows key by accident and couldn't maximize the game anymore. So I killed it and reloaded.
In this save, all fleets are still there. I have zero logistics though, so I can't create new ones (I guess this part is the expected result of the plague, though that was not clear to me initially). Like described aboves, I can neither control my existing fleets nor get the ships in them.
PS: Researching the cure did not change the situation, the fleets were still defunct.