I've heard some horror stories about people transferring their SD card ACNL info from the 3DS XL to the New 3DS and having corruption issues. I can't recall if the people who lost their saves after this transfer were using a digital version of ACNL though. All I know is that I plan to backup my save before I insert my game into the New 3DS.
I have too. I actually waited to transfer mine until I got my Sandisk SD card because I was paranoid I wouldn't have enough space on the new XL's default. I also didn't do any partial transfers for the same reason.
I'm guessing if you had unstable nets maybe it could corrupt, but I would think that would damage more than just Animal Crossing.
Some guy on Youtube was claiming he tested things on multiple DS's and claimed that if you keep the digital copy running for more than 2 days straight without a 10hr break, apparently it corrupts. Not something I believe, honestly. Others are saying the Reset trick causes corruption, but the person who mentioned this also kept bringing up Resetti, and if you're getting Resetti while plot resetting...well you're not plot resetting. So not only did that person sound unintelligent, but me and many others plot reset constantly and have never had an issue.
I have a bit of a hunch that the corruption may be caused by the SD cards Nintendo ships out on its systems. Perhaps they're faulty? It would explain why the problem is so widespread but also not so widespread. Many of us tend to replace the SD cards because space is so limited.
My only other guess is maybe it's just a cart that got messed up during shipping or general use, or maybe the card is defective or damage, or maybe the 3DS itself has some damage. But Mitzi doesn't seem like the irresponsible type so I honestly sort of doubt damage is at play. My only guesses are:
A) The default SD card has issues
B) The Cart and/or SD card were defective
C) Really really bad luck
All I can say is it's such a cruddy situation and I'm glad Mitzi's taken it well, but I really wish we could narrow down the reasons this happens. It's the missing child glitch from Animal Parade all over again (That one took months to solve @_@)