Dfault said:
If not, then the photons arrive at detector #1 in exactly the same state as they were when they were first fired from the photon gun
No, they don't. The experiment with the atom present is a different physical configuration than the experiment with the atom not present, and that makes a difference in the wave function of the photons at detector #1.
With no atom present, we can take the wave function of the photons at detector #1 (which is the only detector in this version of the experiment) to be identical with the wave function of the photons at the photon gun. Strictly speaking, this is not correct for any real experiment; in any real experiment there will be some nonzero probability that a photon hits the wall instead, or otherwise fails to reach the detector. But we are idealizing away all those complications, and with that idealization, every photon emitted by the photon gun reaches the detector in this version, and the wave function of the photon is unchanged.
With the atom present, however, the wave function of the photons at detector #1 is no longer the same as the wave function of the photons at the photon gun, because there is now a nonzero probability amplitude for each photon to be absorbed by the atom. From the standpoint of detector #1, this is no different from a nonzero probability amplitude for each photon to hit the wall instead of detector #1, but unlike that case, we can't idealize away the nonzero probability amplitude for each photon to be absorbed by the atom, because that's precisely what we want to experiment with--what happens when the atom is present. So we have to take that nonzero probability amplitude into account when analyzing the experiment.
However, it's important to understand what this does
not mean. It does
not mean that photons that hit detector #1, and are not absorbed by the atom, still "interacted with the atom" in some way and had their energy changed (any more than a photon in the no-atom version that doesn't hit the wall on its way to detector #1 still had to "interact with the wall" in some way). All it means is that, if we want to analyze what happens when each photon is emitted, we have to take the photon wave function emitted by the photon gun and split it into two pieces: one piece to represent the possibility that the photon will be absorbed by the atom, and the other piece to represent the possibility that the photon will not be absorbed by the atom and will hit detector #1. And both of these pieces of the wave function have
different energy distributions than the wave function as a whole. The first piece, roughly speaking, has the same energy distribution as the energy level transition in the atom; and the second piece, roughly speaking, has whatever is "left over" in the photon gun energy distribution once the first piece is subtracted. So the second piece will have a lower expected energy than the photon gun distribution as a whole, and that is what we will observe at detector #1.
Now, as I said before, this particular experiment doesn't actually have any real quantum weirdness about it. What I have said above can be understood reasonably well as just a simple classical process where the atom preferentially absorbs photons of higher energy, leaving those of lower energy to be detected at detector #1. There are no quantum interference effects involved. But it is still true that you cannot attribute a definite trajectory to each photon, you cannot say that photons not absorbed by the atom still interacted with it, and you cannot say that each photon has a definite energy when it is emitted by the photon gun. So it is still true that classical reasoning, if applied too literally, can lead you astray.