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It should replace boot.ini or any other critical system files that get deleted by a virus. I only mention that because unless your going to back up your hard drive or system directory wholesale, theres no point in backing up any 'system' files.
BTW its not normal, even though people say XP just 'does that', for any files to just 'disappear'. You should check your system completely for any unknown processes, trojans or viruses, and do a complete security lockdown. Beyond malware or tampering, the only reasonable explination for registry corruption + missing files is filesystem corruption. Check your hard drives completely as well, including the surface scan.
You should back up your registry hives, since those are techincally user generated data. You can install a fresh XP and overlay the old registry hives to restore most applications to functionality.
You also will want to back up your files in "documents and settings\username". If you do a completely fresh install those files will restore your desktop, application data (bookmarks, etc) and start menu.
Beyond that try to keep your own human generated data completely seperate from the windows system areas, then you can just back up those two things and whatever folder you keep your work or personal data in and always be assured that you can recover from a complete wipe and reinstall with minimal problems.
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