I have a question like "Why is it often assumed that particles are found in energy eigenstates?", it is a little different, though.
When one solves the hydrogen atom, one can use a polynomial Ansatz and derive the energy eigenfunctions with that. The energy differences between the eigenstates are exactly the energies that are observed in spectroscopy. So it seems to me that atoms are in a pure eigenstate before and after the transition.
If the state was a superposition of two eigenstates before the transition and a different one after, would the energy difference still be a difference of $E_n$?
Say $$|\text{before}\rangle = \frac1{\sqrt2} \left(|1\rangle + |2\rangle \right)$$ and $$|\text{after}\rangle = \frac1{\sqrt2} \left(|0\rangle + |5\rangle \right).$$
Then before it is $\langle H \rangle = (E_1 + E_2)/\sqrt2 $ and $\langle H \rangle = (E_0 + E_5)/\sqrt2 $ afterwards. The difference would be something which is not simply $E_n - E_m$.
One postulate of quantum mechanics is that each single measurement is an eigenvalue of the operator. So even though $\langle H \rangle$ could be something arbitrary, a single measurement would have to be taken out of the $E_n$? How does this relate to the energy difference (the emited photon) having energies of $E_n - E_m$?