Does "Noindex" lead to Loss of Link Equity?

[M_D_Golden_Peak]

Our company has two websites with about 8,000 duplicate articles between them. Yep, 8,000 articles were posted on both sites over the past few years. This is the definition of cross-domain duplicate content.

Plan A is to set all of the articles to "noindex,follow" on the site that we care less about (site B). We are not redirecting since we want to keep the content on that site for on-site traffic to discover. If we do set them to "noindex," my concern is that we'll lose massive amounts of link equity acquired over time...and thus lose domain authority...thus overall site rankability. Does Google treat pages changed to "noindex" the same as 404 pages? If so, then I imagine we would lose massive link equity.

Plan B is to just wait it out since we're migrating site B to site A in 6-9 months, and hope that our more important site (site A) doesn't get a Panda penalty in the meantime.

Thoughts on the better plan?

[wrttnwrd]

I believe EGOL answered this one:

http://www.seomoz.org/q/noindex-follow-is-a-waste-of-link-juice

However, I wonder - can't you just use rel=canonical. That works cross and intra-domain.

[M_D_Golden_Peak]

Thank you, Ian.

We thought about manually setting the canonicals on specific pages of site B to be the URL of the same article on site A...but we don't have the bandwidth to do this for 8,000 articles...plus, we're redirecting site B to site A in @ 9 months anyways. Really just looking for the best short term solution to protect site A in the meantime from Panda updates targeting duplicate content.

EGOL gives a good breakdown of what he thinks is best. Thanks for sharing that link. I guess I'm dummy for forgetting that the "follow" portion of "noindex,follow" allows link juice to be spread to the pages linked to from the "noindex" page. That makes logical sense...but will it protect our domain authority? I would think so, but don't know for sure. If anyone is more certain than I am, please do add a vote of confidence