If the lead locomotive cuts its brake valve in and attempts to set the brakes while the mid-train helper still has its automatic brake valve cut in and in the running position it will be trying to pump the brakes off at the same time the lead engine is setting them. Not a good plan. Only one locomotive should have its automatic brake valve cut in at a time.
If the train has a mid train helper and is moving upgrade to get water for the second engine and the mid train engine has control of the air the lead engine needs only to shut his throttle and set his independent brake to bring things to a stop.