DrDu said:
What I didn't see in your comment, but what I thought to be one of the most important points having been brought up in the discussion, is the fact that while the ground state of hydrogen + gravitational field has a formal expansion in terms of the field free eigenstates, this does not mean that hydrogen gets into instable excited states as all realistic changes of the field will be so slow that one ground state will be adiabatically transported into the other.
Lebed explicitly assumes that it's adiabatic. Yes, I think it's pretty clear that there's something wrong with his interpretation, since his predictions are contrary to the results of experiments.
I haven't been able to convince myself that there is anything trivially wrong in his arguments. His calculations show the atom changing its state adiabatically, but the locally observable properties of spacetime haven't changed, so it's no longer in the ground state. This is different from a normal case where, e.g., you adiabatically apply an electric field, so that the observable properties of the space become different.
My paper focuses on the comparison with experiment, but what I would criticize about Lebed's theoretical work in general is that his papers are silent on a lot of issues that obviously beg to be addressed. His calculations are coordinate-dependent, but the reader is left to guess what coordinates are required. He doesn't address what happens to a system when it undergoes a collision, and this makes it hard to believe that his experiment, as originally proposed, would have worked, even if his calculations and interpretation had been correct. He never seems to have considered the effect from solar gravity, which is trivial to calculate and nearly the same size as the effect he proposes for a space-based mission. He describes the calculation of probabilities of excitation, but not radiation rates; the only reasonable thing to do in order to calculate a rate seems to be to take the time derivative of the excitation probability, and presumably there is no radiation when this derivative has the wrong sign. When you calculate this rate, it depends on the dot product ##\textbf{g}\cdot\textbf{v}##, which clearly violates the equivalence principle (OK, he claims that anyway) but also seems likely to violate Lorentz invariance.
Some of the things that seem to go wrong in his work, such as likely difficulties with conservation of energy-momentum, are not really difficulties that are specific to his idea. They are present more generally in semiclassical gravity. There are a lot of problems with semiclassical gravity:
http://arxiv.org/abs/1304.0471
http://motls.blogspot.com/2012/01/why-semiclassical-gravity-isnt-self.html
http://backreaction.blogspot.com/2012/01/real-thought-experiment-that-shows.html
http://relativity.livingreviews.org/open?pubNo=lrr-2008-3&page=articlesu4.html
See Lubos Motl's blog post for a nice discussion of energy nonconservation.