Einstein would like a word with you
Neither mass nor energy can be created or destroyed. They can be exchanged for one another, but this typically happens (on a macroscopic scale) inside a nuclear bomb and not a helicopter. The helicopter and human expel the same amount of gas over time that they ingest. It might be a different gas, but weight is a function of mass and not volume. The energy comes from chemical reactions and not breakdowns on the atomic level
The scale only cares about the direct force that it has to apply to keep the box from accelerating downward. In this case, the force depends on the weight of the box and whether or not the helicopter (and thus the system, in physical terms) is accelerating up or down.
A more abstract explanation of the experiment can be found
here.