It happens sometimes when I bump my the back of my 3DS against a solid object or carry it around in my purse/pocket. So far no damage beyond just losing whatever progress I hadn't saved at the time. I make it a point to save whenever I finish doing something important just to be on the safe side.
Well, with the update. You have to have an SD card. (I think...)I have removed the game card and my sd card not knowing I was on the game
I was scared to death, but my town was okay in the end
I got my game card removed a few days ago while it was still in. I thought my game corrupted, but it didn't. Phew. But is that what happened to you?