Not sure if this needs to be in spoiler tags since it's part of the main storyline, but it contains spoilers up until the church.

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.