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Generally, trains are scheduled so that one train decelerating roughly coincide with another accelerating. You can plan ahead and orchestrate all you want and overcommit capacity as much as you want. Leftover that didn't cancel out is fed back to hydroelectric dams for gravity storage which do require cleaning but are immune to chemical degradation.

By the way, implementing regen on synchronous motors is relatively easy, IIUC, command a positive torque to the inverter and it draws current and line voltage gets pulled down. Command negative and opposite happens.