No, but you have to ensure that you copy the save data over asap. Basically, what happens is, when you write to the save file, it writes some identifier to both the save data, and to the 3DS internal memory. When the game loads a save file, it checks that they match.
If you backup your save file, and then play, the next time you save there will be a new identifier in the 3DS memory. Now, if you try to use your backup, that will have a different identifier, so the save will not load. Hope this is understandable.