Ah so, I am up to the part where you are supposed to go to the sanctum to become a keeper, however if I do then I just kneel there forever. I followed the quest marker instead and found the guy stuck standing in a field behind the sanctum. I could still ask him about the cycle and stuff but he just kept standing in the field.
I suspect it may have something to do with me changing the cell respawn timers. I did so because the alchemy ingredient and enemy respawns were too long for me, I used up all my alchemy ingredients and couldn't harvest any more in the area around ark. Or perhaps the cell respawn is an unrelated problem.
However it seems that the player house resets if the cell respawns and the magical symbols come back. I collected a symbol I definitely collected before and it counted towards the total 100 I'm supposed to find. And I paid for the marketplace house to be refurnished again.
Does anyone know if cell respawning is a problem? Or remember which console command you are supposed to use to reset an npc? Was it just disable then enable?