I bought the buy 2 get the third day free tickets from
UT and was able to upgrade it easily - only paying the difference between 3 days and the Annual Pass. So, I did get credit for the day I didn't pay for as well.
I think the difference is if it's a Universal promotion ticket or a regular ticket that just has a special deal on it. My tickets were regular tickets with a special deal. The third day free was an
undercover tourist thing. The current buy one day get two days free ticket is a promotional ticket through Universal so I'd expect you would pay the difference between one day and the AP price for that one.