I had the same problem, I thought that it was because I switched DS's (my GF has a fat, I've got a thin and we share the card!).
Took the DS-X from Fat, to thin and it had created 2 new BLANK gamesaves... I'm guessing the old gamesaves are lost.
Booo.... Got about 2/3 of the way...
although i ended up accidentally changing my nand with no way of going back bc i didn't know you needed a gamecube controller to restore it (i have a wii minus/1.1, which doesn't have gamecube controller support)
and if i find the sd card i have my NAND backed up on, i can not only restore the NAND if i solder the right part in, but i can also put my NAND on dolphin, then i can play dolphin online, like PMEX Remix or MKWii Riibalanced