We study a relatively simple model of atomic dark matter in which an atomic rearrangement process can occur, resulting in the emission of dark photons. In this paper we study the detection of these dark photons in neutrino observatories via their kinetic mixing with the SM photons. We study two different scenarios, one in which these dark photons are emitted today, and the other in which the dark photons were emitted during galaxy formation. In both cases we find that neutrino observatories are the best probes of this scenario and produce significant bounds even when the dark atoms are a negligible fraction of total DM.