All the engines are doing is changing their power output automatically to maintain the required NR. They don't really care what position the collective is in. During those stages of flight that you mentioned, if the aerodynamic forces on the main rotor are causing it to accelerate one way or the other, the engines are just going to automatically compensate accordingly (to maintain a constant NR), even though the collective position remains unchanged.
Same reason why if your MGB is in the process of seizing that you'll see the torque steadily rise to maintain NR despite the collective position remaining unchanged. Eventually when the engine power maxes out you'll then see NR start to droop. I don't think what you are seeing has anything to do with control rods moving in response to airframe flexing.
The FADEC is just a constant speed N2 governor, all it really cares about is maintaining the correct engine output speed. Sure, it knows the position of the collective control (I'm guessing there is a collective position sensor in the flight control system somewhere), but this is just an "anticipation" function so that when the collective moves, and at what rate, it knows to give the engine an extra squirt of fuel (or not), as determined by the control software. Collective movement is just fine tuning the metering of the fuel, a collective in fixed position is not influencing the FADEC to do much at all.
Last edited by gulliBell; 3rd May 2016 at 05:25.