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Wait did that meteor have jutsu negating abilities that we didn't know about? No it didn't. It's not going to negate a jutsu like Edo Tensei. Yes the jutsu did stop for the arms that were gone it's why they didn't come back.Can you really say that every bit of his soul is bound to each part of the body? Because if that were to be the case that would mean that cut an arm off means tha part of your soul on your arms is on "hell". In the end edo tenseis still were made through a living body that can be completely destroyed but the soul remains on this plain, Madara had his entire body destroyed by his own meteors while he was an edo. If it was actually null the jutsu edo tensei would have stopped the moment it touched his body, why would it only null part of the jutsu and not the whole thing? An Edo's arms are no jutsu they are just part of one but while a jutsu still exists it can be remade.
To begin with Chakra is already linked with spirit because its made of spiritual energy so destroy chakra is technically destroying part of ones spirit