Could be the WinSXS folder, which can be HUGE and is based on hardlinks which are easily upset by a change in port ID.
Being hardlinks, the chances are good that the "missing" space was never really missing, just a reporting error. (Not that it's excusable. Microsoft has yet to even acknowledge it as an issue....)
Ahh, I hadn't thought of that. I suppose that could be it.
Do you have any prior experience with port changes causing problems with hard links? I don't know much about how hard links are implemented internally by NTFS, but in *NIX file systems (e.g. ext4) the port ID is irrelevant when creating hard links.
If the world isn't making sense to you, you're either drinking too much or not drinking enough.