IIRC there is some proposal stuff in the missing episode. When they aired the next episode, there was a scene that referred to something that we had not seen. Presumably it was in the previous episode and since it didn't air, we are left wondering. It was mentioned in a scene where Hodgins was asking Booth for proposal advice. In this scene it was clear that he already asked her once and was wondering what to do next. I assume that the first proposal was in the missing episode. They can remove stuff from the unaired episode to make it fit better when they do air it, but they really can't fix the episodes that refer to something in the un-aired episode.