Read what larsonm wrote above. It makes no sense in what you're trying to do. Move your parent VM over to new vCenter 6, take a new snapshot. Now Create a new linked clone pool pointing to the new vCenter 6 server and use the new snap you just took, now spin up all your linked clones from that pool and get rid of the others. Switching from automated to manual is only for FULL cloned desktops.
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