A system and method for separating a vehicle system into separate vehicle segments, separately moving the vehicle segments, and re-connecting the vehicle segments without initiation of a brake penalty application are provided. The system and method communicate a suspend command signal between vehicle segments to suspend operations of vehicles in a cooperative mode. The vehicles in the vehicle system are decoupled into plural separate vehicle segments. The system and method also move one or more of the vehicle segments separately from one or more other vehicle segments. The vehicle segments are reconnected to form the vehicle system, and the system and method communicate a reconnect command signal between the vehicle segments to resume operations in the cooperative mode, without incurring a penalty brake application of the vehicle system.