Decoherence dynamics of quarkonia is studied in the high-temperature deconfined phase of SU($N_c$) gauge theories. In particular, we analyze the symmetry properties of SU($N_c$) stochastic potential model and find a novel event-by-event symmetry for $N_c=2$ case, similar to the $G$-parity of hadronic systems. This novel symmetry constrains the relation between diagonal and off-diagonal components of quarkonium density matrix, leaving the latter to be finite at late times. We also present one-dimensional numerical simulation of the model, which indicates the usefulness of the complex potential simulations for the quarkonium survival probabilities in relativistic heavy-ion collisions, provided that the effect of dissipation can be neglected.