Unless this was back in the Win98 or DOS days, deleting your config.sys is no problem. Your config.sys is used to load drivers before the kernel loads. So back in the day you would load drivers to see more then a few K of memory, or the drivers for your CDROM, etc... But that was only important on operating systems that used DOS as a kernel, like Win95 or 98, and possibly ME. But WinNT/2k/xp all load system level drivers on their own...
Now in days it would be better to lead them through tearing apart their registry, expecially since there is no undo. But again, if they have XP they would have System Restore enabled by default, which backs up your registry.
Squick
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