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.
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. :)