You should be Ok to get the difference back, lemme share my experience.....
I bought my annual pass this year and two days later bought into DVC. Not realizing I was entitled to the discount (about $100), I didn't say anything till I came home and read some other DIS posts.
Next trip (5 months later) I stopped by a Guest Services booth in DTD and asked about it. I got the difference (something like $100) refunded to me in cash since that's how I'd paid. Got a new pass printed up, same expiration date, and was on my way with the money in a matter of minutes.
So I'm sure you'll be able to work something out with them also. Good luck!