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On Thursday we reported that the backlink data was out of sync in the redesigned webmaster tools. Well, over the weekend, that was fixed.
Googler, Jonathan Simon said in a Google Webmasters Help thread that it is now up to date. Jonathan said:
Check out your site's backlinks data in the new version of Webmaster Tools. We've just finished the process of loading the most recent backlinks data so you should now be able to see all your site's backlinks.The backlinks data between the new and old versions of Webmaster Tools may not match 100% but the new version's data should be more comprehensive for most sites.
Some people are still having issues, so if you are one of those, join the thread and Jonathan or Sagar can help you.
Forum discussion at Google Webmasters Help.
