I had an R4DS and now I have an AceKard 2. I put the games and save files in the game folder but the saves are not recognized. I tried renaming them (adidng .nds before .sav) and it just refreezes when trying to load the game.
It could be that Acekard stores the saves on a folder or another place other than the R4DS does. I switched my microSD card with my R4 saves and games and put it into my CycloDS and everything worked just fine.