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The easiest way to do this these days is probably a modded 3DS using an app called Checkpoint
There's also a DS app called Savegame Manager but you need either an original DS or DS Lite and a DS flashcart to use it.
For modded 3DS systems, I also want to mention PKSM: https://github.com/FlagBrew/PKSM which is a Save Game editor for DS and 3DS Pokemon games. In short, you can copy the save file from your Emulator (may also need it to convert to .sav format) onto the SD Card of the 3DS, tell PKSM where to find the save file and then use it like Pokemon Bank to transfer (or edit) Pokemon to any DS and 3DS Pokemon game.
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- Options to back up and write saves to and from cartridges and memory cards?
- Just a friendly reminder to backup your saves. Regularly. If you can. And your save states.
- can i transfer my save on a hacked switch to a clean one?