As simple it is this is just one line of DOS command to recover the files being hidden by some virus and unable to see even if you enable to show hidden files option. This mostly happen to USB drives and Portable heard disks.
Nature of the issue:
Your folders will be gone and you will see shortcut files with the folder names but they will open a file explorer insted of your actual folder.
Solution is simple:
1. Open a Command prompt at the location where your files were.
2. Type the following command,
attrib -r -s -h * /S /D
3. Wait for it to do the magic.
And you will have all of your files.