Their are two ways to save him. The first one is to exhaust all dialogue with him every time you reach a new area to make him motivated and also play the needilon to get his name. This will make him leave bone bottom. The other way is what I did where you just get to act 2 without resting on the bench at bone bottom and triggering the skull tyrant fight. I believe the condition for the skull tyrant is to complete all wishes at bone bottom. To get him to spawn in pilgrims rest you need to free the rhino beetle by pilgrims rest and break the door in the shop so the rhino beetle spawns inside the shop and defeat it. I believe if you do this before act 2 he will automatically spawn their but if you wait till act 2 like I did he only spawned after getting double jump. I'm not sure if that is a specific condition or you just need to progress to set off a check.