On Feb 7th, 2013 Google announced a known issue with the links counts
found in Google Webmaster Tools. It may appear that you have lost most of your links but its just a glitch and Google is working on the problem now. In the meantime, your traffic will not be affected.
Above is a snapshot of the Links to Your Site page in Google Webmaster Tools and below is a post that Google made on the Webmaster help Forum a few days ago.
Known issue: links to your site data issues
Thursday, February 7, 2013 | 2:23 PM
Labels: links
Some Webmaster Tools users have reported missing data in the Links to your site section. We are aware of this issue and are looking into it; you do not need to take any action. We hope to have the normal data shown again in the near future. The data were shown there is informational and does not affect your site’s crawling, indexing or ranking.