I have the download version of Pokémon Moon. Let's say I wanted to start a new save file without deleting all of my old Pokémon. I know you can't use an SD card from one system on another, but is there anything stopping me from creating a back-up copy of my SD card's contents, then copying it back onto the SD card to reset my progress to the state it was when the back-up was made?
( I read that someone asked if this was legal. Yes, it is. As you are just modifying the hardware you bought. However, using PIRATED Games using Homebrew, is Illegal. Don't use Pirated games!)
Yes. This is possible, However for this you will need to install Homebrew. Homebrew is a Custom Firmware that allows stuff such as:
Custom Themes, Roms, Save Managing and Manipulating (Export a save, Create Pokemon on your PC using PKHeX, Then Import the save) (Or just export the save and it will be there) Etc.
I recently reset my Omega Ruby since I didn't know what to do in Sun, so I felt like replaying Omega Ruby. But Since I had alot of Pokemon on there, I made a backup using JK's Save Manager. If you would like to install Homebrew, Don't just mess around in your 3Ds Files, but instead look up a video.
Here's some links I found for u.
https://wiki.gbatemp.net/wiki/List_of_3DS_homebrew (List of Homebrew Apps that work with Homebrew)(How to use PKHeX and Save Manager with Sun and Moon. This is probably what you want. You can export the save and just leave it at that.) (How to install Homebrew on Any 3DS)
(I recommend to also save the files on your computer, So in the case something goes wrong (Rare chance), You won't lose your saves!)
Glad to help