All saves, custom firmware or not, are stored somewhere in the "Nintendo 3DS" folder. If you want to back up your saves so they will work on any NAND, use Save Data Filer. If you want to back them up and you do not plan on formatting, backing up the "Nintendo 3DS" folder will be fine.Is there a folder in the SD card that has all savegames for cfw so that it can be transferred to the pc ? I am using rxtools but will switch to aureinand someday but not now since i am waiting for things to progress
And if i Format the 2ds everything would be lost too