A Josephson junction, formed between two phase-biased superconductors and a normal metal, hosts a discrete spectrum of Andreev bound states (ABS). In this paper, we develop a theory for long ballistic Andreev interferometers in two-dimensional metals. We consider three frameworks in our theoretical analysis: (i) perturbation theory in the tunneling amplitudes; (ii) non-perturbative transport theory; and (iii) physically motivated approximations to visualize the conductance maps in the (flux, voltage) plane. We find a non-standard phase-sensitive Andreev reflection process in ballistic interferometers that couples the supercurrent to the non-equilibrium populations of the ABS in the normal region. Furthermore, our model shows that conductance spectroscopy follows the spectrum of the ABS in long junctions. We also discuss our results in terms of the semiclassical theory, the classical orbits being the one-dimensional Andreev tubes. Our theoretical analysis captures the results of recent experiments by the Penn State and Harvard groups.