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In this case site B is not a new site. I am not moving all traffic to site B only a portion which included duplicate urls that were software generated between domains.

I went ahead and added the links to the sitemap, however when google crawled the links I receieve this message. When we tested a sample of URLs from your Sitemap, we found that some URLs redirect to other locations. We recommend that your Sitemap contain URLs that point to the final destination (the redirect target) instead of redirecting to another URL. However I do not understand how adding the redirected links to the sitemap will remove the old links.

Another explanation might be that there are some session ID parameters that are being indexed and totally inflating the internal links to page metric. If you have an ecommerce site or something that is adding session IDs, you could have a huge number of links to the page that are in truth the same link, and Google is recognizing this. Have you looked at the details of those internal links?