this feels more like a physics thought experiment rather than something related to aerodynamics.

Your concern is apparently not about what happens in the "air" tank, but about energy annihilation somewhere. This not about aerodynamics. If I misunderstood, then clarify (and perhaps shorten) your question.

In chamber A the kinetic energy of the rotor (due to its rotation) is dissipated in heat/friction with air + potential energy + deformation energy upon touchdown (which, in turn, goes in heat). In chamber B heat/friction is missing so that a higher energy goes into deformation. Is this your doubt?

I don't believe this has anything to do with aviation or aerodynamics. It is a not completely defined thought experiment that can have endless discussions and disagreements because of the missing details. We're not going to revisit the take-off on a treadmill question either.

May I suggest you apply Occams razor and remove everything that is superfluous, such as propellers in a Vacuum chamber? There is nothing "holy" about the conservation of energy, it is much more absolute then that.

@sophit If you didn't skip that word, you would know that its bearings are rough.

@PaulSmith The bamboo dragonfly in the vacuum chamber is necessary to exhibit the ideal situation expected by the law of conservation of energy.

@DeltaLima If you want more details, please note that the airplane treadmill question is short, and this question was already felt to be too long and everything superfluous should be removed.

This is ridiculously complicated, misses the only part that could possibly make it on-topic (calculation that would give QA<QB), and remains completely off-topic for this SE regardless.

@Americanboy how the bearings are doesn't make any difference, if they are rough more energy gets wasted in friction/heat in the bearings, that's all.

"What happens in chamberA (...) is that two energies (...) collide and some of the energy is annihilated": That's a statement that you, OP, should prove, before asking someone else a demonstration starting with "you have to show me".

@Americanboy I guess I don't get what difference in energy you're trying to point at. In a vacuum, the device will not be slowed by air resistance, so it'll hit the target surface harder, so it'll cause more deformation (eventually heat). The shaft's rotation will come to a halt due to friction with the hole, the blades will eventually spin down (how long that takes depends on the bearing but all the contained energy has to be released, so the roughness of the bearing is actually not relevant).

@DarthPseudonym Your description of what happens in chamberB is very accurate.

Both dragonflies consume the same amount of electricity, sooooo ...