Well, I just found out you can't do a native query to perform deletes (learn something everyday :-). I get this after a createNativeQuery("DELETE FROM...") / executeUpdate():
java.lang.UnsupportedOperationException: Update queries only supported through HQL
I'm at a loss as to how I can delete the relationship rows from RELATION_AB while leaving ENTITY_B rows intact (e.g. I just want to remove the relationship, not the entities in that relationship).