Yeah, Josh made a comment on an earlier commit about this...he said that we actually should probably use Update_attribute or similar calls that invoke callbacks, throughout the merge process, because "We don't want the merge tool to have to know whether or not sp_application (or any model) has callbacks. It'd be safer to use update_attribute everywhere in the merge process instead of update_all."
  For now, I want to get this into production, so I am not going to update all the other update calls, but I guess this 'could' be a project for the future...not sure how important it has to be...