John mueller confirmed that they are aware about this and expecting report to return to normal in the coming days” as Google’s Webmaster Tools search query reports has bug now.
The Google Webmaster tool stopped showing data on September 23rd. This came shortly after Google stopped passing virtually 100% of referrer data to webmasters. Google implied the bug was unrelated and promised to fix it soon.
I currently am able to see data from September 25th and going back, so this is a two day improvement from when the bug was first reported.