I'm curious if this has taken on the role of something else? Like.. he returns to these thoughts when he gets upset about other things in the relationship, but because he has this old fall back emotional situation, he goes to that instead of trying to figure out how to feel about the new situation? I've had this happen to me. When I realized it, I started asking myself "Okay, what are you really upset about?" and that helped eventually shift away from thinking about it at all.

I also think he has to truly want to move past these thoughts in order to actually move past them. He has to consciously make an effort to stop himself from thinking these things (which is really hard, I know). Purposely distract himself. He might be using it as... almost self punishment? Or because something about it is making something (subconsciously) feel good or feeding some need he has?

This is really something only he has control over -- there's nothing you can do (or even should feel like you have to do... You've done nothing wrong).