Duplicate content on a site is not grounds for action on that site unless it appears that the intent of the duplicate content is to be deceptive and manipulate search engine results. If your site suffers from duplicate content issues, and you don't follow the advice listed above, we do a good job of choosing a version of the content to show in our search results.
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You just need one [Name]VirtualHost with multiple ServerNames in your Apache conf (or to forgo VirtualHosts entirely if these are the only two domains being served from this machine). Assuming you're running Apache. It sounds like currently you have two [Name]VirtualHosts with different DocumentRoots. But it's difficult to say exactly what you need to change without much more detail as to your current configuration.
posted by enn at 10:22 AM on October 1, 2008