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We sell complete sites including the domains to several partners that create content that is shown together at the main site. What we want to achieve is that the main site copy is the original but the others are indexed as a partners copy.

The way we want this to happen is that the search results point to our partner sites but never to the main site while the main site gets all the credit for any links obtained.

We are trying setting the main site article with a noindex, follow and a link to the partner article, and in the partner article we have a rel=canonical pointing to the main site article.

Are we correct or the noindex at the main site will break the canonical reference?

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What do you mean by "gets all the credit for the links"? –  Lèse majesté Feb 9 '13 at 15:33
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Google cannot verify the canonical reference when that reference is not in its index. Logically it should break but the best way is to test it with 2 domains. Check the below comment and the discussion http://www.seomoz.org/users/profile/211048 as it relates to this point.

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