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Well, now the redesign is complete, and I have no idea if or when Google would unmerge the domains. Domain1.com has plenty of incoming links, so I guess Google would pick it up next time they do a deep crawl?
Tried everything, from shutting down urls, perm redirects.
Nothing works. To me, it seems impossible.
I just put all the urls that Google had merged back together. And now Googlebot is hitting my site heavy and pages are showing back up.
Pages are showing up again, but, under the old url, and not the one I want to promote, but it's better then all the mess of trying to get them unmerged.
Just leave them together, but try to get your incoming links updated.