There is a type of virus that makes your folders disappear, turning them into .ink shortcuts instead. The husband of my colleague encountered that virus recently...
To make sure this is the same problem you are having, here's a description:
There is a very annoying virus from Indonesia that is quite dangerous. My colleague's husband encountered that virus. He plugged in his mobile storage device into someone else's computer and BAM! All his folders were gone, replaced by shortcuts of the same name. That virus actually converts whatever folders you have in your storage devices and turns them into shortcut icons (.ink files). Is this the same virus you are having?
Once you encounter this situation, do not panic! Your files are still there, not deleted. You can just use a simple way to get all your files back: