There have been a number of complaints throughout webmaster forums noting the link count in Webmaster tools keeps returning dramatically declining figures. There was even one case study of more than 1.5 million links not being registered after just a two week period.
This news has raised alarm among those in the SEO industry. More and more SEO consultants are noticing the link drop and are becoming concerned. With the above example, there was a 45% drop in the reported links from Google’s Webmaster tools.
More alarming than that, there have been other reports of as much as an 80% drop in links according to Google’s accredited link count. According to Google, this is a known issue and will be working to rectify as soon as possible. Google have also assured site owners that the information provided with Webmaster tools is purely information and won’t affect the website at all in terms of crawling and indexing of pages.