There was a recent bug reported by some webmasterworld guys regarding homepages of sites dropped from the index, Many sites out there lost their homepage due to some kind of duplicate content penalty, Google Guy who is mostly regarded as an important representative of Google replies to it, Here is his response:<\/p>\n
Hey bakedjake, I think I’ve found your problem. There’s no penalties or anything like that; it’s because you’re splitting your internal linkage between two different root pages. Suppose your domain is yourdomain.com. Do the search [site:yourdomain.com inurl:https]. See those 912 https results? Click on the cached page for the first one. Now mouseover the link in the top left. Instead of pointing to <\/em><\/span>http:\/\/www.yourdomain.com\/,<\/em><\/span><\/a> notice that it points to <\/em><\/span>http:\/\/www.yourdomain.com\/index.asp.<\/em><\/span><\/a> All the https cached pages that I checked link to the index.asp version of your home page, and there were enough of your internal pages doing that that you convinced us that <\/em><\/span>http:\/\/www.yourdomain.com\/index.asp<\/em><\/span><\/a> was the canonical root page for your domain. That’s why when you do the search [yourdomain] you see <\/em><\/span>http:\/\/www.yourdomain.com\/index.asp<\/em><\/span><\/a> as the first result.<\/p>\n So your hundreds of internal https pages pointing to a different location is clouding the water some. If you fix them to all point to the same location (http:\/\/www.yourdomain.com\/) then we’ll crawl all those pages in a little while, and you should be fine shortly afterwards.<\/p>\n