You will have to ''seek and destroy'' the bad folder.
I hope you don't have many folders in your main SD directory,select 2-3 folders and right click to see if you get huge amount of memory used,then narrow the search till eliminating the bad boys
It will not work by searching any folders, you will not find those lost space. It is just not there. As others suggested you can copy all SD contents to PC, and format SD, then copy back, you can have all your lost space back.
That's so far the only way to handle it. But in future you will get lost again...