The temperature changes with friction and pressure changes are very predicable with a good thermodynamics treatment from a Thermo textbook or Engineering Handbook. This is fairly straightforward when operating away from a phase change condition, but get much more complex when shifting through partially saturated two-phase conditions.
All that being stated, It makes sence that since you are simply scaling-up a functioning pilot system. You could calculate your pilot plant system plumbing Reynolds number and size your scaled-up production system, with Reynolds number guidance, to have the same or lower pressure drop to avoid excessive heating of the fluid in your plumbing.
Pressure drop will always cause a temperature rise proportional to flow. I used this in a test stand to heat oil to 300 degrees F, and not have any risk of overheated heating elements. My customers were amazed, and then very pleased, that it worked very well. The mechanical equivalent is the temperature rise in friction brakes as they slow a vehicle. There is a formula to convert mass flow multiplied by pressure drop across an orfice to temperature rise, unfortunately I don't have it handy.
What I find amazing is that there is a pump able to produce that high a pressure at a flow rate high enough to cause heating.
I am surprised at the little faith that your scientist and chemist colleagues had in your setup. I would that they would be smart enough to know that you weren't heating the water on purpose and that there would be a solution somewhere. As you stated you need energy to make heat and removing that energy would remove the heat and save the molecules.
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