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ive imagined them making a single game with both versions available to play, say for example- they release "Pokemon Red and Blue" and when you start the game you can choose to play through Red version or Blue version, and each Switch profile will get to choose whichever version they want. you will have the option to switch versions, but only by deleting your save data.

the funny thing to remember is that the carts will not carry save data, everything will be stored on the Switch, so its going to be a big change in how Pokemon save files get managed no matter what happens