Yes... you can cut them in place. No... you will not be able to control the height as you suspect. To get an accurate measurement, they have to come out.
Secondly... you DO NOT cool a spring in water. You only cool it in ambient air or you will drastically change the temper of the spring steel and they will end up to be useless when your done.
And lastly... its not worth taking a chance with kinetic energy. Simple tools that can be affordably rented from a local parts store is much cheaper than replacing a door or window... or you head, for that matter.
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