Dude files missing after Windows 2000 reboot.

I rebooted our Win2k server after some Windows updates were done. The Dude would not start because the exe was gone. The directories were there but no files in them. I reinstalled and restored maps from a Dude backup. Has this happened to anyone? Any ideas as to why this happened?
I had Dude version 3.6 installed.

antivirus ?

Yes, I use AV and there is no malware on this server.