NTFS Permissions Vanish?

It's that time again for James his latest bizarre issue.

So we're working on this one lady's computer remotely, been working on trying to get her offline files to sync properly with the server she remotely connects to over VPN, and along the way, we keep discovering that her entire C drive loses ALL NTFS permissions, seemingly randomly and without warning.

And when I mean all, I mean all -- you check the security tab, and there's not so much as a system user in there, totally blank.

Any idea what could cause the entire C drive to just up and wipe out all permissions like that?

Setting the permissions (everyone full control?) on C: and having all subdirectories inherite those permissions?

Restoring an FAT32 diskimage and converting it to NTFS afterwards?