Well, there was a threat that Dumbledore reminded Harry and Hermoine of; that if they hadn't returned in time it could be fatal, how exacty, I don't know. I belive that if they returned within the same room once the mission was completed that their dna would morph together again. However, I guess we may never know the mystery of magic, will we?
Or maybe the 2nd set of H and H would just disapeaer onto another dimension. THat would be cool. And their souls would remian in this dimension. I think it would have to involve their souls b/c clearly JKR recognized this part of human/wizard/witch with the demenotr's kiss. In the end, their souls we returned to them, I figure.