I made that same mistake with my DSi, when I traded it in for the 3DS. Granted, it was only a few - kinda crappy - games. Nevertheless, they're gone forever!
The way it's set up now, though, is easier. Even though my Wii-to-WiiU transfer was somehow corrupted, I was still able to go in and re-download all my VC and WiiWare titles on my WiiU. It was a pain in the ass, but at least it was possible.