Okay so I had a little run in with loosing Serana during the main storyline of dawnguard. I also didn't see a fix for it other than reloading a recent save or waiting for about three days, which by the way didn't work for me. I decided to try and continue with my little journey to find Serana. Well the silly little vampire decided to go on with the next quest instead of going back to the dawnguard castle. I found her at the ancestor glad where you have to read the elder scroll. So next time she goes missing, and you go looking for answers, try going on with the quest line. I don't know if its a fix but I tried several things and all I had to do was go and find her at the nest quest. Try that and see what happens! Also if anyone else has a fix that may work for others, post them here!!!