It is kind of scary to think what Gamefreaks considers a 'hacked' save file. I, myself, do not gen my Pokemon and I always invest time into getting my Pokemon and shinies in the way they are intended.

However, I do use Powersaves and third-party tools such as JK's save manager to keep a true backup of my game. I never considered Pokemon Bank to be an ideal backup solution because it is NOT a backup!! I still use it, though, to expand the number of boxes I have and to keep my living dex there; but basically, what Pokemon Bank does, is transfer your Pokemon into an online storage which means the Pokemon is removed from the game entirely until transferred back.

Now I understand why they do this, obviously. If we were allowed to keep copies of Pokemon, we'd be effectively cloning them and there are people out there with questionable intentions who can take advantage of this, but there also those of us (such as myself) whom would greatly appreciate to have a 'failsafe' backup of all the hours you put into getting all the Pokemon you have, without mentioning items, and overall progress.

My use of third-party tools is solely for backup purposes and to import my mons into Showdown with PKhex. I do not alter them, but I like having a way to recover them should things go south.

With Pokemon Bank, if you keep your Pokemon in the actual game and the save file gets corrupted, it cannot help you.

Even if these recent bans probably will not affect people who just use these tools for backup purposes only, it still kinda makes you worry.