I did 3 reservations in Feb....points for a week, then cash for the weekend, then points again. We had them all linked. Same with October, we had 2 reservations, since we had to waitlist for 2 nights. They do tell you when you book that there is always a possibility you have to move, but I never had to go check out and then check back in....it was treated as one reservation for us. Even our room cards with charging crossed over the whole stay and we had one charge at the end of the stay.
I think as long as they link them, you are fine and will not have to check out then back in.