About nine days ago Webmasters started noticing an issue with the link report within Google Webmaster Tools. Then the issue grew and more and more webmasters noticed a bug in Webmaster Tools where the link count dropped significantly from what Google typically reported on their site.
As you can see from the screen shot below, from 3.8 million links to 2.1 million links then to 1.3 million links and now we're back at 3.8 million links:
The links reports are probably still settling down for many webmasters but like I said originally, things would go back to normal.
Forum discussion continued at WebmasterWorld and (one of many) Google Webmaster Help.