Flow compensation, the slicer feature you seem to be talking about, is about the material properties of the thermoplastic you're printing - its thermal expansion and corresponding shrinkage when it cools, as well as how much the extrusion path cross-section deviates from the ideal model the slicer uses to determine how much material to extruder. It is a percentage to compensate by.
Flow rate is how much volume of material you can push through the nozzle per unit time, and typically has units of mm³/s. I think what you're getting confused by is that CHT enables a higher flow rate - this means it lets you push more material through the nozzle in the same amount of time. That has nothing to do with flow compensation and does not mean you should change it.
In theory it's possible that you've upped your flow compensation to compensate for slippage in the extruder gear from already trying to go faster than your extruder can really push, and that you no longer have to do this with a CHT. But that was a really sloppy compensation to begin with, if you did it, and would have led to really inconsistent, speed-dependent extrusion.
I suppose it's also possible that the differing melt consistency from a CHT will make the extrusion path cross section more closely match the ideal, which could affect the optimal flow compensation to use. But I have not seen any evidence to that effect.
In short: you don't need to do anything with your flow compensation. Whatever you saw about CHT and flows was not talking about flow compensation.