Does saving in Aether Paradise corrupt the game?

Solution 1:

Ever since generation 3, the save system in Pokemon has had a soft-backup of sorts to protect against corruption (and probably cheating). You likely closed the game and returned to the home screen before it had finished saving - interrupting the save.

If the system is turned off mid-save (or some other action interrupts the save), when you load again the game will load the backup (previous) save if the main save is corrupt. In some generations it will actually tell you this is going on.

It can be assumed that before it saves over the main save, it copies the existing main save as a backup then saves the game over the main save. When loading it would check the integrity of the main save, then load the backup if it's corrupt.

It's not fool-proof, but it's better than nothing.