It depends. Which version is it? Do you have the game card or is it the digital version? The digital version has a save file checker that checks to see if you're running the latest save or not. The game card lacks such feature.
If it's the game card version, use svdt
https://github.com/meladroit/svdt/releases
download the svdt.3dsx, svdt.xml, and svdt.smdh and put them in SD:\3ds\svdt. Then launch homebrew, launch sdvt with AlphaSaphhire, and you'll see a file called "main" under your game card. Save that to your SD card. (Pressing Y copies it I think) "main" is your game save. Don't delete 'main' from your game card, instead just reset your save in-game. To restore, just highlight "main" from where you saved it in your SD card and re-copy it to your game card.
However, if you have the digital version of AlphaSapphire, then if you try to back up your save and restore it, your file will corrupt.
Also, do not worry about my uncertainty with the buttons. It has a list of controls when you first boot up svdt