I did something similar back in August. I modified our reservation online and changed from a Florida Resident discount to an AP discount, saving us $10 a night. When I originally made the reservation, since it was room only, I was only required to pay a 1 night deposit for the reservation. When I got my final bill at the end of our hotel stay, there was a credit on that for the original deposit amount, and then each night that we stayed we were billed for the lesser nightly amount.
So in my experience, no, they did not put it back on my credit card, they just credited the deposit amount paid to the hotel account.