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We have a large site too and we have different sitemap.xml files for different sections of the site and submitted in WMT where we can see which sections are having indexing issues under WMT > optimization > sitemaps Maybe that is a good thing though, do you have 3.4 million legit pages or are dupes getting filtered out? Has anyone changed your parameter handling or coding on the site URLs, or robots.txt file or noindex meta tags?