Eytan Suchard said:
It definitely depends on either you are a Lagrangian or an Eulerian observer.
Even though it is since Nov. 2, 2018 you posted your comments, I am now responding in case you are still interested. At first I did not understand most of your statements, but I think I understand them now after a little studying, so I will restate what I think you said in my own words.
(1) The Lagrangian observer sees the photon maintain the same wavelength when it is reflected between two mirrors as the mirrors drop down toward a source of gravity. This is because the Lagrangian observer travels alongside the mirrors as they descend. But the immobilized Eulerian observer measures just a short segment of the photon's path on one level and again at a lower level. The observer sees a blue-shift in the photon at the lower level. Without the GR conservation of energy requirement included, the photon has gained energy according to QM.
Eytan Suchard said:
In other cases such as the expansion of the cosmos, we may say that the gravitational energy that mass gains as the cosmos expands is on the expense of red-shifted photons that reach far observers from the photon source.
In the expansion of the cosmos, the loss of energy during the photon's red-shift is transferred to mass -- an inadequate explanation of dark energy's force which is accelerating the expansion of the universe.
Eytan Suchard said:
The big picture of conservation cannot be understood from GR alone and physics may have to be updated. After all, physics is a predictive language and language is not reality but a human interpretation of reality.
Conservation laws use higher order derivatives than Noether's first order derivatives in her Lagrangian equations. Conformal gravity mathematics use yet higher order derivatives. QFT uses first order derivatives and makes accurate predictions, through the standard model, that may nevertheless be wrong at Planck scales. New conservation laws will be found at Planck scales. GR is incomplete with respect to the full explanation of energy conservation laws, and physics may have to be developed further to gain a complete explanation of its subject matter.
I have had the good fortune to have heard that all knowledge, including physics and its models, is a virtual reality which can never be the same as what is physically real. For example a five ton tree is not the same as its virtual reality visualization in the three pound human brain.