Tried rebooting, nothing. By uninstall and re-install, you mean delete the directory and files and then extract them again from the zip file? If so, then just tried that (also gave the new directory a different name just in case). Unfortunately it didn't help.
Thankfully though, the other games I made 3dns for are still okay, I was afraid moving the games directory might mess them up too. I'm guessing what caused the problem was starting up the game while the 3dn was gone (strange as that may sound).
Guess I have to start over with that game :\