I don't know which warning beep you're referring to but open control
panel/Sounds and click on the Sound tab, you'll find a list of things
and their associated sounds, you can change or disable the ones you
don't want.
The best way to disable the warning sound would be to switch to Linux. Try
Damned Small Linux. That should work. If not, there's about 300 other
Linuxes you could try. And don't forget the tarballs. You need them too.