cart saves always transfer over. so if the game saves to the cart (most 3ds and ALL DS do when using a cart) they will save to the cart using a flashcart, and when you move the cart the save goes with it. note that the updates, streetpass data, and any DLC save to the sdcard, so they won't transfer over, but you can always just reinstall the update. you would need a system transfer to get legit dlc to move over.
