My guess is that it's a filename issue. I use an R4i Gold 3DS and by default it names its saves like "nameofgame.nds.sav", meaning if I try using save formatted more like say "nameofgame.sav" my roms won't see them. So assuming the new one doesn't use an entirely different save format, what you can try is just playing any game you don't already have a save for, save in-game, then check out how it formats the filename on the newly created save and see if it differs from the formatting on your old saves.
"I think that the problem with this video is it is highly derivative of many popular bands within the genre. Although when viewed on its own merits, it does have a deeper groove. However what it has in groove, it lacks in originality. One can't help but be reminded of such bands as Pearl Jam, White Zombie, Suicidal Tendencies and other bands that bear the mantle of so called "Alternative Rock". One is even reminded of Lorie Anderson when she wore curlers. Hehehmhm! This video speaks less to the heart and more to the sphincter. In closing, I think Korn would do well to learn more from -"