Meta Rate My Team PokéBase - Pokémon Q&A
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i've almost reached the 100 mark on my Friends List, and since I can't remember who is who (in-game) I want to format my 3DS. problem is, i'm not sure if it'll erase my Pokemon Data for X/Y. if so, I CAN'T format it, 'cause I have a shiny in X, and TONS of H.A. Pokemon in Y. so I need to know if I can format it w/o losing any data JUST for those games.

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If you want to format just so you can reset your friend list, just manually hop in and delete all of your friends after writing their friend codes down somewhere. Then, ask your friends (irl or chatroom) for their friend codes again and cross-reference the codes they give to the ones that you wrote.

DS and 3DS game data is saved on the game card itself. (Source)

This means you'll still have your precious shiny and HA Pokemon in the game cards. Pokemon data will not be deleted. Just be sure to eject the game cards before the format. It will only delete things having to do with friends, like your Safari or Acquaintances, and eShop titles.

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thanks so much! BA + Up-vote! that makes me feel SO relieved. now when i'm done catching ONE of every Safari Pokemon in EACH of my Safari's (64) i'll format.
Also if you were concerned about the data on your SD card, only backup data is saved on it.
I've been reformatting my 3ds and 2ds for a while. Not only is your game(s) safe, so is your e-shop account. I still have my $11 Also, all the stuff I downloaded, although is deleted, is available to just re-download, no cost. Just be aware your Dream Radar progress, and probably progress on other downloaded stuff, will be erased
Thank god it works, I lost my pokebank but my pokemons are safe <3