A client of mine was showing 0 indexed urls in Google Webmaster tools this morning, out of 6000 urls. In panic mode, we eventually found out that Google Webmaster tools has been having this error since this morning. This is from Google’s own blog.
The indexed URL counts for Sitemaps that you have submitted in Webmaster Tools may be showing zero (0) indexed URLs for some sites. We are aware of this issue and are looking into it; you do not need to take any action. This will have no effect on your site’s performance in search results.