The Dragonborn rebirth process seems to allude that such things would be removed or cured somehow, or would they be incorporated into the new Dragonborn form in such a way that they would be part of the new form?
Things that I can think of that would fall under this include Willing Deformity, Grafts, and Draconic Feats... I think there are more but I can't remember off the top of my head. Basically any physical aspects acquired beyond your normal race. I guess this could include some templates too.
If many of these would be overridden, how would you compensate the player for giving up things they spent feats, gold, and perhaps even levels on?