Hello, A few months ago, I could see several hundreds of links to my PR4 website. In one day almost all of the links were removed from webmaster tools. Then after some times just a few links reappeared. The website is still PR4 and getting a relatively acceptable (for the content and rank) from google (several hundred) but the links are not shown in webmaster tools. This has happen to only one of my domains. Has the webmaster tools messed up? What should I do because webmaster tools has become almost useless for this specific domain (since it does not show the useful information anymore). Mac
These things happen when you get many number of links from a same website under different category. Initially the search engine index every backlink come from the site. Gradually the search engine refines the worthness of the pages and drops several backlinks.
The links were not from same websites. Actually those were from very reputable websites like download.com, dmoz.org and many other important websites. Those websites still produce visitors. Besides normal serach shows those links and even "linkto" command in google search shows links which are not listed in webmaster tools.
Thanks for the clever answer ipexpert. So that what happened to some of my backlinks. I guess a lot of blogger and administrators are in the same boat as we.