In order to know for sure, some experimentation has to be done. It would involve testing all known variables, like model, wi-fi on or off, etc.
One test I did involved me using a spare 3DS that I transferred all my stuff off, with a digital copy of the game, wi-fi on, and I reset around 11 times, trying to emulate the conditions. None of the 11 resets seem to cause any damage at all.
So I don't know what the connecting link between the stories are. Is there a common factor?
I've done the reset trick at least 1,000 times between my two copies, and used the home button to close the game off. I never have had any save corruption issues, and I've had the game since day one.
There's no system backup with a cartage
SD Cards are no different if I understand what I've read on other websites. Animal Crossing has this really stupid save system that makes it impossible to truly back it up. Here, let me quote someone who has more knowledge than I do.
"I had heard that Animal Crossing New Leaf's save data has a double encrytion. Every time you save, the game creates a new key for the SD Card save data, and the 3DS internal memory. Today, I did a test to confirm and backed up my "Nintendo 3DS" folder on my computer. I inserted the SD Card, opened Animal Crossing and saved. I put the SD Card on my computer, and deleted the "Nintendo 3DS" folder (I should've backed up this one aswell but forgot).
I copied back my backed up "Nintendo 3DS" folder and opened AC, and the result was as I expected... The save data was useless and wouldn't be accepted because it wasn't the same.
This got my attention and I noticed that it was a very selfish move on Nintendo... just so people couldn't copy/back up AC Save Data and clone... However, this is also a big flaw aswell! If your SD Card got corrupted, then your "Nintendo 3DS" folder backup would be absolutely useless... Thus, all of your effort in AC has gone to waste."
Pretty much, you have no way to back up your save because Nintendo doesn't want people restoring their save to a previous session when they had all their valuable items before trading. So, they completely made it impossible(until the system possible gets hacked and you can perhaps edit the ID creates) to even back up your digital copies. The back-up tool won't work on it for the same reason.