External hard drive missing files

So one second I was in my hard drive and everything was fine, and the next second when I tried to go into It again, I noticed many of my files were missing but not all and my disk space was open, This happened out of nowhere, it was simply just sitting there, the only thing I can think of is that i was downloading a bunch of screen shots the I purchased(not torrented) and right about that time when they finished DLing is when it happened.

So I tried to eject the drive and restart my comp and insert again like another thread recommended but that didnt work, then I tried to do the "show hidden folders" in the contol panel, nothing still. finally I used Recuva and that I think worked, I have recover all my files but they are just the files and not in there proper sub directories..is there anyway I can fix this or use some kind of software that restores everything and puts it in its correct place..or am I asking too much?

I appreciate any help, thanks!

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