I don't have first hand information on upgrading because I've never done it. I did suggest to my neighbors, however, to buy tickets through way.com. They purchased 3 day/1 park per day tickets. After they arrived, they decided to upgrade them to hoppers. At the ticket booth, the CM talked them into upgrading to deluxe APs instead, and they got the full value of the 3 day tickets, even though they had purchased at a discount through way.com.
Different situation then what you're asking about, but I think you will receive full value. HTH!