The so-called malware actually is a line of code from WP for getting emails to post. So that's not it. And I deleted the line of code just to clear that error issue.
I exported only the affected category, and then deleted only some of the articles in the category. I re-imported the category - and the import showed that the articles already existed (I turned off the cache and deleted the cached filed). I checked - and none of the articles were imported.