This is not about security but being secure. There are two things you can do with Windows 2000 to keep it running...
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The first is to make an ERD, done by going to Backup in the System Tools/Accessories/Start Menu. You might have to boot the OS with the four boot disks to repair your system with the ERD.
The second is to go to the DOS prompt and type sfc.exe after WINNT/SYSTEM32. Your options will appear on your screen. This program can, if enabled, keep your main system files, including all the Microsoft updates -- if they are digitally signed -- intact and as the originals, safe from other programs you install!