1. I would go from steady state to steady state as you suggested.
2. The potential energy change that occurs on the difference in elevation of the submarine may be used to account for the energy transfer to the hull
3. Minor point - the neutral buoyancy condition is when the weight of the volume of water displaced by the submarine is equal to the weight of the submarine. As the submarine shrinks in size it will displace less volume and you will need to compensate more by shedding the weight of the trim tanks by pumping more to the ocean