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Earlier I was reading this question,

Is there a way to move Pokemon from a ROM to a Physical cartridge?

It talked about Pokemon Black and White, it also mentioned that in the 3ds games there was some software implemented in terms of safety features and I was wondering if there was any way around it. I want to find a way to transfer Pokemon from Sun and Moon romhack to the main games as simply and safely as possible. If any one has an answer it would be greatly appreciated.

I require a list of the software and/or external devices you'd recommend along with directions on how to use them for a citra rom to the main games if at all possible.

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Yes! There in fact is!

  • (BIG NOTE) If your game is within Citra, and the official game is within your 3DS, you will first need to hack your 3DS to run Luma3DS Custom Firmware. Follow the guide at 3ds.hacks.guide.

  • Place JKSM Save Editor on your newly-customized 3DS SD CARD from here (https://github.com/J-D-K/JKSM/releases), place it in your system, power on, and install it using FBI's CIA installer. This will give you the upper hand now. Turn off your 3DS and place it in your computer.

  • Right click on Citra and export your Pokemon save. Then, right-click it again and open Save Data Location. Place all contents within this folder from your computer into the SDCARD\JKSM\Saves(game)(create a folder here)

  • Put your SD card back in your 3DS and open JKSM. Go on SD/CIA and search your game. Press “Save Data Options” then press “Import Save” and then finally click on the folder with your name and save within it. (I would name it citra). Finally, slap that yes button and you should be good to go, provided you followed the instructions correctly.

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    Note: This should be the safest possible root, but when moving saves, nothing is fully safe. You take each action at your own risk. Use JKSM to backup your save if you don't feel 100% about replacing. If anything goes wrong you can always restore your save if you made a backup.
    – WG481
    Jul 28, 2021 at 2:50
  • I will look into your recomendation but i was also wondering if i would be able to trade the pokemon via the ingame trade mechanics, also if i customize the cartridge will it still work the same way the game would if it was uncustomized, and would it allow me to change the shiny chance from 1/4096 to 1/100 and vice versa. I want to make sure that im not compromising my device or my games because if i do then i have to spend more money than I might need to. Thank you for your input, and i will definitely look into it but i want to be as safe and non-damaging as possible. Jul 30, 2021 at 14:50
  • You cannot edit the data on a cartridge unless you dump it @ErikEveritt. The games on the carts are ROM, not RW. The Save is a different story. PKSM can edit the saves, but not change the shiny chances. Checkpoint can be used to load shiny cheats, but sometimes fails. After dumping the cartridge, you could freely edit the data and repackage it at no extra expense.
    – WG481
    Jul 30, 2021 at 20:36
  • Ok that sounds much better, Thank you so much for all of your help! Aug 7, 2021 at 21:07

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