Sorry, perhaps I wasn't clear enough. Only card1 type games (those that save to an EEPROM chip) were broken, Pokemon XY/ORAS are card2 type games (card2 games save to a writable portion of the ROM itself).
Oh I know the Pokemon games are card2, but from your post it seemed like you meant all physical carts and card1 roms.
Anyhow thanks, I actually remember importing with sdf my physical copy of DKCR3D and then exporting it to a .3ds rom. There was no error, but for some reason it didn't write the save to the rom, even though it said it did. Good that they've fixed it now.