New info: apparently games like Animal Crossing do indeed have a way of seeing if your save file isn't the one you last used on the system. There is a system in place where a piece of data (in my opinion a checksum value but more on that in a bit) is placed both on your sd card and the system's internal memory (most likely in "extra data"). Those two files are synced each time the game is saved. If one is out of sync with the other, the game will know that something's been tampered with, and won't play the save file (I assume you'll still be able to play the game, but you'll need to start from scratch).
I think the file that's in sync is a simple md5 checksum or something. That way the game will be able to tell not only if the save files didn't match up...but also if someone happened to hex edit the data and tried to give themselves extra items or something. For those who don't know...a checksum is where you run a file, files, or zip of files through an algorithm to create a unique identifier (a long string of numbers and letters that is unique). If any sort of change happens to any file that was put through the algorithm, the result would drastically and unpredictably change. The algorithm's results are impossible to predict or fake which stops someone from somehow creating a forged identifier. Once the identifier is made, (for example H2459) it's result is saved on both the system memory and memory card. If someone tried to load an old save or an edited save, the identifier would change to something else like (Q2f15) and when someone tried to play the file on the 3DS, the check to see if the identifiers matched would fail, the game would know something was up, and thus you wouldn't be able to play the file and would have to start over. This system of preventing edited saves seems to be able to be used selectively, which is why up till now no other save files have had this check (which is why my previous experiments to play with save data succeeded). So games where duping or hex editing would influence the online components of a game's gameplay or economy can use this feature to prevent cheating, where games that are single player and meant to be played alone can benefit from being able to have saves copied and replaced.
Whew...that was fun to explain...anyone follow me?