It seems that your hard drive is attacked by virus.
Sometimes, the virus would hide your files inside the drive, mark them as file system and create some related shortcuts. So you cannot find them.
Therefore, here are my ways for you to fix your problem:
<1>. Show the hidden files or folders as below:
Start => Run => Type in “control folders” and press “OK” =>Click “View” and hook “Show hidden files and folders”=> Press “OK”
<2>. Recover your data at the aid of a third-party recovery tool, if you cannot show out all your files.
I would recommend you to try a hard drive recovery freeware to regain your data. This freeware helped a lot as my flash drive was attacked by some vicious virus last time. It had recovered all of my wanted data back.
<3>. Format your drive to keep it clean and usable.