The spent approximately $600 million on those trains for all intents and purposes of replacing the R32s & R42s that were still remaining pass their useful life. So yes they will stay and serve the transit system for the long haul. It wouldn't make any logical sense at all to pull them of again and restore a car fleet close to 60 years of age back into service. The R179s are still relatively brand new even after two years so there still some kinks they have to troubleshoot on. They continue to check and maintain any viable aspect of the R179s so they'll get it together moving forward. The R142s which were made by the same builder as the R179s (Bombardier) had there issues early on as well, as did other subway car fleets. Despite all the mechanical flaws, bottom line at this point and time the R179s are needed and the can pick up the slack once the warranty on the R179s expire.
There's no need for the blame game towards the T/Os or train crew in general. They are quality trained to know how to operate and control the movement of their assigned train. Unless there's more to it with said "Black Box", T/Os don't deserve to be scapegoated. The Bombardier techs from what I've heard don't grab as decent as the Kawasaki techs do when applying the braking system into a station and in bad weather it's the same issue with all the tech trains.