During the fight with Evelyn, Zombie Jake died. He was in a sea of poison which somehow turned into a sea of fire due to unfortunate, unavoidable circumstances. He was turned into a pile of ashes. In most games this would be a reload but I thought it would be okay to continue on with this game.
Just today I got to the church. In the room before the skeleton boss I ran with a perfectly alright (for a zombie) Jake and a man lying in a bed. Jake helped me in the boss fight but I was not able to talk to either of them, before or after the fight.
I haven't played a game without him "dying" the second time, so I'm not sure what else might not be working.