Disappears from where? What listing?
It seems you are able to find them again after boot up. You said that as long as you do not shut down, the folders and files are operational, so that assumes that after boot up you find them somehow. How do you do that?
Suddenly after more than two years,my toshiba P25 S676, xp, sp3, upon booting up, folders disappear. Any Folder alphabetically preceeding the folder "Documents and Settings", disappear and cannot be found. As long as I don't shut down the computer the folders and files are operational. After shut down and booting up the folders disappear. I have put all kinds of folder names on the c drive all of which disappear if they alphabetically preceed Documents and Settings.