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This work is concerned with the problem of planning trajectories and assigning tasks for a Multi-Agent System (MAS) comprised of differential drive robots. We propose a multirate hierarchical control structure that employs a planner based on robust Model Predictive Control (MPC) with mixed-integer programming (MIP) encoding. The planner computes trajectories and assigns tasks for each element of the group in real-time, while also guaranteeing the communication network of the MAS to be robustly connected at all times. Additionally, we provide a data-based methodology to estimate the disturbances sets required by the robust MPC formulation. The results are demonstrated with experiments in two obstacle-filled scenarios.