We just returned from our trip and we had one of our cancelled reservations show up on My Disney Experience. I just ignored it. We never received a reminder for that reservation, like we did for the other ones, and I was never charged the $10 for not showing up. But you could try calling them and see if they can fix that for you.
The funny thing was when we went to the restaurants to check in, three of the 6 reservations ended up under my daughter's name instead of mine. I had booked all of them.

But it worked out fine.
I was able to use the app to cancel a dining reservation while we were waiting in line for Test Track. My DH said that he really didn't want to go to that restaurant that night. So I hit the cancel button and it was canceled - very cool.

It was a lot better than trying to call central reservations.
I liked using the My Disney Experience to check on wait times. And the park hours changed in response to the unexpected crowds. They had added another MSEP and extended hours on Sat at MK. So it was nice to have the app for that. It also told us when a ride was down.