arXiv:2610.19390v1 Announce Type: new Abstract: In this paper, we present a novel multiscale formulation for the Optimal Transport (OT) of large swarms. The scheme is divided in two levels, a top-level OT formulation with a terminal penalty cost to handle time-varying densities, and a low-level, Model Predictive Controller (MPC) that allows agents to track the nominal velocity under control affine dynamics and rejects external disturbances. We show that the terminal-penalty dynamic formulation reduces to a regularized static dual, which agents solve in a distributed way to compute the nominal velocity.We also prove distributional input-to-state stability in the $1$-Wasserstein metric of the density flow with respect to the mismatch that the low-level and the target motion introduce, so that the tracking error only perturbs the macroscopic flow by a bounded, quantifiable amount. Finally, we demonstrate via simulations the effectiveness of the proposed method handling time-varying targets and state perturbations.