Do you have a cartridge of pokemon Omega Ruby?
I don`t know if it will work, but you can try extrat your save with save manager(homebrew), restore the save to the cartrige game, start the cartridge game and save and import your save with Save Data Transfer Tool.
After transfer the save using the app from e-shop, start the cartridge game and quit to be able to restore the save using the save manager(homebrew).
Don`t forget to make a save backup from your cartridge game on your pc to restore after that.
