i had a fairly similar issue with my new leaf cartridge. basically all updates were stored on my flimsy sd card, and my 3ds failed to recognize it, so my system offered me to update, otherwise i couldn't start the game. i did, and upon finishing it went "oh oops we actually don't have an sd card to store this on!" and kept erroring me out when i tried to start new leaf. fixed it by basically doing a factory reset on my 3ds, which was ouch, but what can you do, really. it miiight be something like this? but then again, i think the game would give them an error, still, instead of just wiping their town data.