Hi
I would try downloading and installing AgentRansack.
It is a very good search engine, once it's installed run a search for some of the files that are in the missing folders as you did before, I've seen Windows not find things, but not AgentRansack even things that were hidden.
If the files have a specific extension search for *.extension, if you know something in the files you can have it search for that along with the extension, for instance, the words registration and serial number found all the documents on my computer about my software registration information, on all four hard drives in just a few minutes.
Have you used any software that hides folders?
I have done this and then forgotten that I hid them, I'm 75. LOL
Check Disk Management and make sure there isn't a partition you don't know about or something strange, see what it says about used and free space etc.
My last idea is to try and run Recuva from Piriform.
http://www.piriform.com/recuva
If they have been deleted by accident somehow, it may find them.
That's all I've got maybe someone else has a better idea.
Mike