Something odd happened to my client's site the other day. He runs a online directory with hundreds of thousands of pages indexed in Google. He have updated the site to a new version, and suddenly, all his long tail rankings disappeared. I thought it might be google hiccup, but ranking didn't come back for more than 6 weeks even with more links built into inner pages. He then did another update, which accidentally created thousands of pages with duplicate titles. We fixed that, but still ranking doesn't come back. He then filed a reconsideration request, and asking if there is any Google penalty, turns out there is none. I am a bit stumped, still trying to fix up all the errors caused by previous updates, but would like to know if anyone have similar experience on large sites and I'd be willing to pay for suggestion that works. Thanks for reading this.
Check for the robots file may be that's applied to the website, along with this also check for what was the last date your website was crawled.
Were any of the links changed along with the update? You might want to check the links from before and compare it now. For example, the backlinks were pointing to an article that was not under a category before like http://www.yourdomain.com/article1, but with the recent layout it is now under a category making the link change to http://www.yourdomain.com/category1/article1 If that's the case then you need a 301 redirect so as not to lose those links. Hope that helps. Have a good day!