So I've just done the part where you unlink NANDs.
I didn't see the part about removing the SD card, and now all its contents are deleted.
Where do I go from here? Do I just reformat the SD with EMUNAND9 and copy and paste the backup again?
@Xdqwerty, Osu! Tatakae! Ouendan! is the Japanese version of the game, different settings/characters/songs but otherwise identical mechanics. I played that before I knew about Elite Beat Agents lol. Both fantastic games https://en.wikipedia.org/wiki/Osu!_Tatakae!_Ouendan