I've had it happen a couple of times, where points ended up refunded and the reservation then appeared as a paid rate - usually it seemed to happen when the hotel made changes to the booking for some reason (in general it had been because they upgraded my room). Only once did I have to explain it on check-out, and a quick look at my original printed booking and it was fine. Hopefully it will be as easy for you to resolve there too, I'm sure it will all be sorted swiftly enough, one way or another.