I want to know the answer (even if I have finished the game) because when I was about to fight Guzma in front of the house in Aether Paradise and I saved and did this:
Saved, pressed home and then got out of the game, then turned off the 3DS.
Then when I went back on the game the next day and I was back at Aether House and apparently I haven't defeated Guzma in Po town so I had to do all that again!
I know I finished, but it would be helpful for future.
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.
It's more than probable that you didn't wait for the save to finish up "corrupting" the game. (More like simply stopping the save, which is a lucky result).
Take your time next time to make sure you get out of the menus before quitting the game.
