They are in the same location at the moment; a "virtualdesktop" folder in the users home folder (Redirected Desktop Folder = \\server\home\username\virtualdesktop\Desktop and the profile folder = \\server\home\username\virtualdesktop\username.v2). I thought the same myself about someone resetting permissions, but I am not very sure. My colleagues does not work with the users home folders or any of the View stuff and our users are not savvy enough to reset permissions on a folder like this situation. And if so, why did the rest of the users home folder or profile folder not lose their permissions. I had to take ownership of the Desktop folder and then reset the permissions from parent to child. The other thing, I mentioned the link clone users and full clone users. The full clone users are all Domain Admins. The link clone users are only standard users (no administrative rights). I understand that standard users can still change permissions of files/folders that they have full control and ownership of.
Going back over my change logs, the only thing I can think of is maybe a folder quota change. We have quota enforcement on the user's home folders. I increased the quota on the home folders last week. Maybe this could have done something weird with that?