I've never heard of such a thing happening on a mac. I've heard of OS 9 viruses (had one myself.) But that didn't come from the net but a fellow student. I don't know. Perhaps someone is gaining access via the net. Keep your firewalls up then to be on the safe side (if you have one.) It is not possible for anybody to delete via LW. But they might do it via some other way.

By the way, sure the files are not invisible? I know it sounds ridiculous but, ... measure the size of the folder to see how large it is. Select closed folder & apple & i keys. Files can be invisible on a mac. Need a utility to change them back. Another option is corruption to your HDD database. Norton Utilities & DiskWarrior can repair those things. Have you tried rebuilding your desktop: Reboot whilst holding down Command (apple) & Option keys & allow it to rebuild.