How will system transfer affect my Pokémon X (and other games') data?

Question

Last Christmas, my friend gave me her old Nintendo 3DS as a present and I've loved it ever since. However, she forgot to transfer her data over. Now, one year later, we've finally gotten together to do that, but now I have things on the 3DS I don't want deleted, but she wants some games she downloaded on her old console to come to her new console.

Two of the things of mine are the Pokémon Sun/Moon demos, but for some reason, it mentioned deleting some things relating to my Pokémon X data. I don't want legendaries or any other Pokémon being lost, since it mentioned something about deleting Pokémon X data. Most of the other apps are hers, most demos but one game she bought.

Would there be a way to change the NNID to mine without deleting things? Is there a way to just pick and choose things to transfer things back to her new 3DS? What would the wisest course of action be?

Answer 1

As for games, the only things that actually get saved local are the updates from the internet. All your data and saves from the game are safe in your game chip. You won't lose all your legendary Pokemon from your game upon transferring over data. Neither will any other game lose their data with a chip.