I have a Windows 2003 R2 Server (running in a virtual environment using XenCenter) that is missing about half a terabyte of space. When I ran WinDirStat, it displays 521 gigs of unknown space being used (see picture below).
I can tell you what this is not:
This is not the System Volume Directory
Shadow Copy is NOT enabled on the Server
System Restore is disabled on the machine
I used Disk Space Fan Pro, it did not let me regain the space
I used cmdassys.exe to elevate the permissions of WinDirStat, that did not work
I ran chkdsk /r /f
I am not sure what else I can do to recover the space. I was thinking it could be offline files, but as a Domain Policy Offline Files are disabled and I can find the directory where they are stored.