If you were checked into the next days flight, then you were not still checked into your original flight. I assume reservations was confused, because the coupon for the original flight was being used for the next day, so it was showing you as checked into that original flight. While some agents try to be helpful by checking you in for a flight the next day when rebooking you, it is basically true that then reservations can't help you. Reservations won't be able to help you with seat, and they won't be able to add you to the upgrade list. In almost all cases, they should still be able to see all of your flights, but there are still instances when even that might not be possible. This is done because the gate agents have much more latitude to do what is necessary on the day of departure.