I think when we saw Boone on 815 in LA X he was already awakened either fully or partially. I just have that feeling. There was odd about the way he seemed so relaxed and he said "if the plane crashes I think I'll stick with you" or something like that made it seem like he knew he had done that before. Bernard seemed that way too when he told Rose that he missed her after just being in the bathroom for a few minutes. That was quite odd.