It sounds like you may not have completely removed the virus, it doesn’t delete the files, but it hides your data folders and shows you fake empty folders. Follow these instructions to remove and repair Windows Recovery, SmartHDD, HDD Recovery, HDD Rescue, HDD Repair and other similarly named fake hard drive repair malware.
Follow these steps in this link one by one, do not skip any.
www.bleepingcomputer.com/virus-removal/remove-windows-recovery
(short summary for experienced virus removers, download and run RKill to kill the malware process, download and run Malwarebytes to delete the malware files.)
At the end, run Unhide download.bleepingcomputer.com/grinler/unhide.exe which should make your hidden folders reappear.
In order to avoid getting these fake system utility malware in the first place, I recommend blocking popup windows in your web browser software, and even better, switching to Firefox with NoScript add on which blocks scripts from running. See the article on browser security here.
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