This paper presents the effects of Discrete Event Supervisory (DES) decision making on aircraft propulsion and flight control systems. The effects of DES decisions in the propulsion system are not limited to the propulsion system control, which is integrated to the DES control unit, but also influence the entire flight control system. A two-level hierarchical DES control system is designed to supervise and coordinate the operation of twin-engine aircraft propulsion. The propulsion system is integrated with the flight dynamical system such that the upper level DES controller serves load balancing of the engines as well as overall health and mission management of the aircraft propulsion. In this paper, the effects of the DES control system on nonlinear aircraft dynamics are investigated.