In the strict sense, it can be accounted for and is therefore not lost. Your friend may not realize that mass itself is congealed energy, so you tell your friend that much more energy in its congealed form is put into the reactor than is put out by the reactor. The force of impact, however, depends on the distance that the rock penetrates into the ground. If we do not know this distance we cannot calculate the force. When we speak of work done, we must understand work done on what, by what.
Work is done on the car by an applied force that originates in the engine.
The work done by the engine in moving the car is equal to the product of the applied force and the distance moved, not the net force that involves air resistance and other friction forces. The ball gives up energy to the air molecules it encounters. This does not contradict energy conservation, for energy is dissipated, not destroyed. The ball strikes the ground with the same speed, whether thrown upward or downward. So they will strike with the same speed.