Unfortunately, it isn't as simple as that. Nintendo has strict rules on system transfers and SD card data transfers, and it simply won't work.
For example, say you have Animal Crossing: New Leaf as a digital game on one SD card. If one backs up the game's data on a PC and opens the game (for whatever reason), the game will start anew. When he/she transfers the original data back onto the SD card, the game will say that the sava data on the SD card is different than the one previously saved, and the original save data will now be deleted.
There are a lot of things that can go wrong, so just don't attempt it. There shouldn't be any legitimate reason why you should anyway.