what is the most efficient way to recover from this duplicate content penalty?

A company I am working with was developing a new version of their site. They put it on another domain of theirs and then put it on their main domain. Except they never removed it from the alternate domain. So we have:

www.site.com

and

www.site3.com

Each of which has the same text.

www.site.com fell in the rankings and I couldn't discover why. Then I realized…

what is the most efficient way to recover from this duplicate content penalty?