I've always worried about this. In a game that you can spend hundreds or even thousands of hours in, there's not really a good way to keep your save data safe. From my understanding, 3DS game saves are stored on the game cartridges themselves, while streetpass data and such are stored on your SD card.
So there's no real way to keep your save data safe. I could spend 500 hours playing this game, and my cartridge could spontaneously corrupt, or break, or get lost or something.
While there is a Save Data Back-up feature, it only lets you back up save data from downloadable Nintendo 3DS software and most Virtual Console games.
What the Nintendo 3DS desperately needs is a way to take save data from the cartridge and store it on your SD card, and vice-versa. This way, I could back up my Animal Crossing data with my SD card, and if my cartridge ever corrupts, I could get a new game and transfer my save data from the SD card onto the cartridge.
Actually, AC doesn't let you backup save data.... I looked at the option myself on my downloaded copy and it says the option is unavailable for this game.