There are too many control surfaces for over-actuated aircraft. The coordination and distribution of the efforts between these control surfaces is a problem, and this problem can be solved by Control Allocation (CA). With CA, the required moment, force, or rate can be allocated to actuators more easily. For one of the over-actuated aircraft, NASA GTM, a dynamic CA method is used in this work. For CA, Weighted Least Square (WLS) equation is used, and this equation is solved with an active set method that can be used with real-time implementation. As a baseline controller, State-Dependent Riccati Equation (SDRE) is used to generate a reference moment. As a Fault-Tolerant Flight Controller (FTFC), CA can be reconfigured depending on the control surface or actuator problem and level. In this work, reconfiguration is especially for the CA's control effectiveness matrix and steady-state distribution matrix. Besides, depending on the problem, especially compensating for an undesirable rolling moment, outer elevators behave like elevons after reconfiguration. Loss of effectiveness (degradation), lock in place (stuck), and control surface damages are studied for emergency cases. Simulations demonstrate that this reconfiguration feature is effective for reference tracking and vital for recovery.