Hello...
I can think of 2 possibilities...first, could the user have accidentally "dragged and dropped" his subfolders to another folder by mistake? Second, go to "View" on the top toolbar and make sure "Folder List" is selected if that hasn't already been done.
If you're talking about missing Personal Folders, make sure that the user is connected to the network on which the personal folders file is kept.
Hope this helps!
Paul