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I don't think you can carry over 1000 Pokedex data in your cartridge.
By the time they've reached that point, cardridges (if they even exist later on) will have more space than we can imagine right now. Also, even when using full 3D models and maps, a 3DS cardridge has up to 8gb of space - that's more than enough to reach Gen VII.
"Evil, beware. We have waffles..." - Raven, Teen Titans