You didn't happen to keep a backup of your previous emuNAND, with all the games working, did you? Then you could maybe replace it and your games would work again, you could back up saves, tickets, etc.
Without a backup like that, I personally don't know if there's anything you can do. I think the two save backup programs only point to installed games, but I haven't actually used smealum's svdt yet so I don't know for sure about it.
I think all you really need to do is delete the contents off of your sd card, which will all be in different folders inside one of the random named folders inside the Nintendo 3DS folder on your sd card. You could even just format your sd card and start your emuNAND over, but you should probably back up any files from your SD card that are not in the Nintendo 3DS folder so you don't need to redownload and replace rxtools/etc..