You need to start the game first in order to do that. Someone can correct me if I'm wrong, it's been a while since I looked at it, but IIRC Ninty's save data transfer tool opens your cart archive with FSUSER_OpenFileDirectly, copies, and then deletes/erases the cart's archive. I was going to try it at one point just for shits and giggles, but then my PC died and I have no way of retrieving the notes I had on path data.
Can confirm. Once I created a new save file, I can now backup/restore saves. Thanks!