Links disappear in webmaster tools – why it happened and how to fix it

We were working on a new site for a client recently when we noticed that the webmaster tools data started to disappear, including the ‘links to your site’ and ‘total clicks’ queries. This website had a gradual increase in links from launch to now, including social media, local chamber of commerce, directory listings etc. Over the course of four or five days, these links began to disappear until we saw ‘no data available’ for total links. We do sometimes see glitches in webmaster tools (WMT) so we weren’t too concerned, but we carried out the basic checks to make sure.

We checked: WMT crawl data, security issues in WMT, site still in Google’s index, still had links pointing to it, no manual actions, both www and non-www versions of site confirmed and verified in WMT.

We searched WMT help to see if we could find anything on missing links – but we couldn’t find anything useful.

We posted on WMT forum and got some helpful replies, including some people saying glitches can affect data for up to 3 weeks. However we weren’t satisfied and went back to the date we first started to see data was missing. Then we realised: the site had an SSL certificate installed then. Of course, this changes the URLs that need to be verified in WMT, to include https://domain.suffix and https://www.domain.suffix

Once we added these URLs, set the preferred version and waited a week, all the data was back and we saw all the links in WMT.

There was no drop in ranking during this period, but it was highly disconcerting! As a result of this, we’ve updated our blog post on SSL certificates for your website: What is HTTPS and why is it important?

So, when you have an SSL secured website, please make sure you have the following all set in WMT:

  • http://domain.suffix
  • http://www.domain.suffix
  • https://domain.suffix
  • https://www.domain.suffix