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How does Zygarde seperation actually work?

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If I seperate it, it says I'd lose him, but can I make entirely new Zygarde out of the pieces that I get from the seperation? By the way, it would be excellent, cause I'm not happy with my Zygarde's nature.

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That's basically it. You can disassemble and reassemble the Zygarde as many times as you wish, with different IVs and natures getting generated each time. However, note that 100% forme Zygarde cannot disassemble.

Hope I helped. :)
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Well you cant have 100% for assembled. It only goes into 100% form in battle.
They mean that when you give zygard power construct that they can't separate