Used space does not match sum of all files

Don't worry, you haven't lost any space. You'll be able to keep saving data until the volume is full - the drive's properties are telling the truth.

The discrepancy appears because Explorer double-counts files that appear under multiple names. Windows uses hardlinks for some system files, and to programs that don't account for that, they appear as completely separate full-size files.

A lot of files in \Windows\WinSxS are familiar/normal system files hardlinked to from other system folders. WinSxS can appear to be fairly large (>9GB on my Windows 8.1 machine), but most of the files in it consume no disk space by themselves. A difference of 5.5GB is entirely reasonable from WinSxS alone.

For more information about WinSxS, see Manage the Component Store.

To explore more about hardlinks (and other types of links), see Hardlinks and Junctions.