Did you do some simulating of fleet battles that turn? The simulator doea a horrible job of distinguishing between fleets created in the simulator and fleets actually present in the game when it's time to get rid of them. I don't think I've seen it actually delete a fleet, but it's not at all uncommon to discover after simulating that a fleet has had all its ships removed. If you don't catch this and add them all back in, the fleet will be deleted in turn processing. For this reason, I always save before simulating with fleets and reload afterwards.
Huge number of fleets? I'm not sure I'd consider 30-35 fleets a huge number. Is that too many for the game?
Douglas, I did some simulator testing that turn before processing, but I didn't use any fleets in the simulator. Could I have messed something else up there?
It doesn't matter how many you currently have. What matters is how many you have created throughout the game. It takes a while to get the naming system to reset back to the first fleet name.