My personal opinion is that he's having a difficult time separating Harry from James and Sirius. The funny thing is, it was always Sirius who had difficulty with that, while Lupin was the voice of acceptance for what is versus what was, as well as very clear who Harry was. In a lot of ways, I feel Lupin's character has been quite altered in this last book. Makes me sad. He's one of my favorites. It would be neat if JK really DID go that route and show his confusion with friend-versus-friend's-son, but I don't hold out much hope as I near the end of the book. I think she's trying to tie up loose ends that don't necessarily need to be tied up.