If anyone else needs a step by step guide how to use their retail saves with a backup of their retail game.
- If the game came with 6.0.0 or newer FW on it and has been played on a 6.0.0+ system this will not work.
- If the save file is smaller than 512kb this will not work.
- Game save will only work on the Same Retail Cart back up.
1. Start the 3ds with the retail cart you want to back up and want the sav file of.
2. Open the gateway menu with "L"
3. Select "Backup 3ds Game Cartridge" (file will save to the normal SD card on the side 3ds, make sure its large enough). Finish the backup of game cartridge.
4. Select "Backup 3ds savegame" Finish the backup of savegame
5. Shut off 3DS and plug the SD card into a computer.
6. Rename the Backup 3ds Game Cartridge extension from ".3DS" to ".3DZ"
7. Move ONLY the Backup 3ds Game Cartridge extension to your RED Gateway micro SDcard
8. Find out the "titleid" of the "Backup 3ds Game Cartridge" by going to
http://3ds.essh.co/
9. Rename the the "Backup 3ds savegame" to the "titleid" of the "Backup 3ds Game Cartridge", e.g Kingdom hearts NSTC is "000400000008D300" so the save file should look like this, 000400000008D300.sav .
10. Do not move the Sav file from the normal SD card (side of 3ds)
11. Plug the SD card back into the 3DS and power on.
11. Boot Gateway into "Gateway mode".
12. Select the game you just backed up (the .3DZ file).
13. Your save should automatically restore itself.
Thank you, nicko , The Real Jdbye and gamesquest1 for helping me out.
I hope someone finds this step by step guide helpful.