I am not sure if anything aside from trying to see files and space on another operating system(like linux)
Windows handles things in a strange way to begin with as an example, If i make a symbolic link to another drive in a folder on d : it will be added to the select all(properties) while not being on the disk. I am not even sure if system restore points show up in the select ALL. Also, some folders simply do not give you permission to see the contents(they show up as ZERO when in fact they contain data.).
In this image you can see a folder that the normal users do NOT have access to, it shows as 0, but if you add your self in the security tab(read only), you can see the size. Are you going to hunt all over the drive for these folders
If you are very interested, You may want to try a live Linux DVD/CD/USB drive to see what it has to say.