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About a month or two after the problem was fixed, there are still no real changes and it remains to be very strange. Searching for the website name, doesnt display the index. It shows only inner pages, and it receives no traffic to the index which SHOULD have the most weight due to the links? I'm continuing to build links for this, but it's just not happening?
Anyone have suggestions or seen something similar in the past?
If it doesn't, is your index page available at the simple domain root, www.example.com, with no redirects involved?
The problem ended up being we referenced the root of our site as www.example.com/ in one and www.example.com/index.html in the other after fixing the second site-map the URL returned to the SERPS overnight.