Who did you email? I have the same issue (was charged for both HDDR and Mickey's Back Yard BBQ even though I pulled my reservation first). I sent an email by clicking on the "COntact Us" link on the Disneyworld web site, and got a reply that said they didn't have access to dining information and I would have to contact the dining folks directly.
I'm VERY hesistant to try to have them cancel & rebook, since there is no availabililty left for either of those shows for the date & time that we have booked. I'm okay with just getting a refund to my card when we go to the restaurant, but I read in another thread that the restaurant may give you a gift card instead of a refund to your credit card? Does anyone know if this is true? That would be fine for MBYBBQ, since that's on the second night of our trip and we could just use the gift card for spending money over the course of the trip. But HDDR is on our last night, and we're checking out first thing the next morning, so I don't know that we'd have a chance to spend it...