PokéBase - Pokémon Q&A
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I already own a copy of both black and white, and me and a friend are doing a playthrough together. Was wondering if buying another copy of the game, would that count as a new save file? Or would both copies boot up the same save file? I own 3Ds XL's. I wanted to have a separate playthrough for a shiny only run.

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I think it is a separate save file because that is the case with the gen six and seven games. I own both oras, two copies of um, and us, and they each have their own separate save file

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Prior to LGPE, save data is stored to the cartridge, not the console. This means that any individual cartridge of Black/White will start a unique save file, even if inserted into a DS that has already played a different cartridge of Black/White.

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If you're going to downvote a correct answer, you should probably explain why.
This is absolutely 100% correct.  I own 5 copies of Pokémon Black alone and can personally confirm this.
Thank you!