Questions
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Duplicate site (disaster recovery) being crawled and creating two indexed search results
It's a little tricky. While Andrea is right about Robots.txt - it's not great for removal once pages/domains are indexed, you can block the sub-domain with robots.txt and then request removal in Google Webmaster Tools (you need to create a separate account for the sub-domain itself). That's often the fastest way to remove something from the index, and if it has no search value, I might go that route. Just proceed with caution - it's a delicate procedure. Doing 1-to-1 canonicalization or adding 301 redirects may be the next strongest signal (NOINDEX is a bit weaker, IMO). However, Google will have to re-crawl the sub-domain to do that, so you'll need to keep the paths open.
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