I needed somewhere to rage a bit, so here we go.
Nintendo killed my save files.
I guess some detail is needed. Nintendo game purchased in the e-shop is stored at an SD card, but tied to the specific 3DS you downloaded it on. Somehow, my oldest SD card has stopped recognizing the 3DS, so I can't access the games even though they are on the card and I have the correct 3DS that should be able to play them. A system update must have messed it up or something.
So now my only option is to redownload the games on a different SD card. The game files are forever lost.