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Transfered Zygarde with 94ish cells from bank to a new game and now I cant see cells. Is this a glitch in the game? Or maybe you dont see cells cores until a specific point and I dont remember?

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Did you deconstruct your Zygarde in the new game?
If I had to guess, I'd say that, assuming your Zygarde was in 50% forme, that only 50% of the cells were transferred. The rest of the cells were in the zygarde cube, were they not? Meaning if you restarted the game and lost your zygarde cube, now the rest of your 44 cells are gone.

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Only Zygarde transfers. The other 44 cells are not connected to him unless you have him in 100% form. The other 44 should still be in the first game.

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Do you have a source?