Welp thats a new one. I just had a character stop existing. I think because they swapped places with a Zoogbat that was despawning, so they both despawned. So that's fun. And it corrupted my autosaves to boot.
Uhh... oops. Yeah, I just checked... bats can delete your party members if they despawn while you walk through them... woops. That's going to the top of the priority list for fixes...!
Were the corrupted autosaves created after your party member was deleted?