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Sudden drop in historical traffic data, after being flagged as a hacked site

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We were recently flagged as a hacked site, appealed the flagging, and it was removed.

 

However, Google Analytics is now showing our traffic over the last 2 years as being around 40% less than what it previously said.  It's as if they went through all the data they've ever gotten from us and retro-actively revised the filtering or something.

 

We have also been measuring traffic internally by other means, and our numbers there have been stubbornly lower than Google Analytics.  After the drop the numbers are a lot closer.  So we're wondering whether Google might have been wrong all along, and maybe they noticed the problem when we appealed the flagging?