I'm not sure there is any answer to "how the photon is lost". How does something move, or exert forces on something else? We observe phenomena, and try to come up with predictive and descriptive theories, but at some point all theories come down to "that's just what happens." What do you want to know about how the photon is lost?
One way of looking at it is, the photon induces reactions that create new sources of amplitudes that interfere with the photon amplitude so completely there there is no longer any net photon amplitude going forward. That's not really right either, because photons are indistinguishable so all we can really say is that the occupation number drops by 1. So that can be viewed as the photon stimulating a process that creates, in effect, a -1 photon. The photon is responsible, then, for its own destruction, in a sense, but it requires the participation of not only an electron, but as you heard above, a system for that electron to interact with.
If you take this view, you can say that to get absorption, two things need to happen. First, the response of the electron must cancel the amplitude of the incident photon, and either free electrons or electrons in conservative potentials can do that (if in a harmonic potential, they will be way better at doing this at the resonant harmonic frequency, and way worse at other frequencies). But to call it absorption, you also have to not create a new outbound amplitude for that photon-- otherwise we'd call it scattering instead. That's where you need some additional complexity-- and a simple conservative potential, even one that binds the electron to an atom, is not enough. There needs to be some competing process, something that can interfere with the creation of an outbound amplitude, such that the photon can actually be destroyed (and its energy shunted over into energy associated with the competing process). That often requires a second electron in the vicinity, which can take up the lost energy (often a free electron, which we then call "collisional destruction" when the free electron interacts with the atom and allows the bound electron to absorb, and not just scatter, the photon).