Pokemon Alpha Sapphire issue: trying to edit the saves have been nightmarish in general for me. Using PkHex itself is very smooth sailing for me. For whatever reason, after exporting the main file back exactly where I grabbed it from (/3ds/Checkpoint/saves/game/name, or when I tried swapping JKSM instead, /3ds/JKSM/saves/game/name), but the game itself is unaffected. What am I missing in this formula?
For reference, I used GodMode9 to extract the trim.3ds file from the gamecart, then installed and deleted the CIA to get the game in digital format on my SD card. Is the save file the game is using just not there?