I nearly shocked myself because after i saved my New Leaf game, i get an error message at the title screen. I thought my game was corrupted forever but it turned out the extra SpotPass data wasn't found.....i forgot to put the SD card back in....
New SpotPass data was created also....silly me....i hope my game is safe.
Happened to me once I was switching carts so fast for a trade I forgot to power off went to main town error, luckily nothing lost...am more careful now though it did happen the other day I forgot to power off hope town is safe but is fairly new for last dreams but still a lot of work into town even if some villagers wouldn't be missed. Should be ok. But on main town scared me bad. Ended up similar to what happened to you and update thing or message.