If you can synchronize arrivals with departures at the same (or a nearby) station, energy regenerated through braking can be immediately used to power the acceleration of another train. If it is not synchronized, the power is wasted (unless they have batteries or some other power cache, which would surely introduce its own inefficiencies).
I once heard a story (though unfortunately I have no references--it may very well be an urban legend) that the Vancouver SkyTrain continued operating through a power outage thanks to (a) its very efficient linear induction motor propulsion & braking, (b) operating at a reduced speed (to minimize the impact of wind resistance), (c) supplementary power from backup generators, and (d) synchronized arrivals and departures from stations in conjunction with regenerative braking. The synchronization could be done precisely and programatically because it is a fully-automated system.