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I was going through Webmaster Tools and I noticed that under 'links to your site' there's only 40 links showing. Down from 700+ yesterday.

I don't think it was anything to do with the quality of the sites linking in because some of them were quite high ranking blogs so I don't think it's Penguin related.

This has happened to me once before on a previous site and after about a month or so they came back, so it's not something I'm super worried about, but it's really odd.

Has anyone else experienced this? Or know why it happens?


Update - All links seem to have returned 20/2/13

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Same exact thing here. This has happened in the past. I believe it happens when Google tweaks their algo. Then it takes time for the next crawl to rebuild all the backlinks. We're down from 6-figures of back links on our primary business site, down to 1400. It is indeed scary though. One more reminder of how our fate rests in Google's hands. I also checked on Digfer.com and we've slipped a couple notches on Google results -- which is putting a dent in our traffic. 'Hoping that's temporary! –  user23132 Feb 5 '13 at 17:16
    
I noticed this also but now they seem to be back like normal. Hopefully they have this situation under control for the next PR –  user23536 Feb 20 '13 at 21:00
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3 Answers

up vote 4 down vote accepted

Its not just you. Here is a thread about the problem on WebmasterWorld: http://www.webmasterworld.com/google/4542427.htm

Here is a thread about it in the Google webmaster help: http://productforums.google.com/d/topic/webmasters/HB8ZdK_DDyw/discussion

This issue has been forwarded to Google engineers who are apparently looking into a problem with the webmaster tools.

Update: Search Engine Roundtable is reporting that Google has fixed this bug as of February 12, 2013. http://www.seroundtable.com/google-webmaster-tools-links-back-16349.htmlhttp://www.seroundtable.com/google-webmaster-tools-links-back-16349.html

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Yep, most of my links just came back. About 70%. –  guisasso Feb 12 '13 at 16:44
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Stephen's answer above is spot on. it seems this is a common problem.

Lets just hope they get a handle on it a little more quickly than they did with the "We Currently Do Not Support This Location" bug in Google Local Places Plus Places or whatever they are calling the maps driven local search now!

I heard rumblings it could be to do with the denied link devaluation update from 17th of January but that could all be a bit tin hat watching the sky's fantasy!

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I noticed my links disappeared from google webmaster however, I can see and validate every single link from open explorer. Obviously since January 22nd 2013, google launched another panda update and I lost ranking position from number 1 to number 2 and some keywords to number 3. I also noticed that my website thumbnail screenshot image on all featured directories has disappeared and showing thumbnail logo instead.. I submitted a new reconsideration request to google after tweaking my content and I received an email after a week stating that google hasn't found any manual spam and it could be their updates.. I guess the site will recover on its own like you mentioned on the main post.

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