Over the past 20 hours or so, there have been numerous reports and concerns over the number of links being reported within Google Webmaster Tools "Links to Your Site" section severely dropping.
The number of links being reported in that section for many webmasters have dropped by as much as 75% for some webmasters.
One webmaster said:
I'm seeing a huge shift in what's being reported by the "Links to your Site" page across all the domains in my WMT account.
Something like 50-75% of Links that still exist and were previously reported are now gone.
Others are freaking out:
Where my all back link gone while I didn’t use “disavow links” tool????
In short, do not worry, it is probably a reporting glitch. It wouldn't be the first time. Google had a similar issue back in August 2011.
So do not worry, you have company.
Update: Google's John Mueller said in another Google Webmaster Help thread that this appears to be a bug. He said:
This looks like a bug or a temporary fluctuation with how the data is shown in Webmaster Tools. Your links are still around and being counted normally within our algorithms (at least the sample I double-checked) -- this wouldn't negatively affect your site's crawling, indexing, or ranking in our search results. I don't have a confirmation from the team yet, but we'll update here as we know more. Thanks for your patience & sorry for the confusion!