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In this study a modular approach to the robust reconfigurable flight control system design for an overactuated aircraft is proposed. The structure of the proposed scheme consists of three parts: a backstepping controller module, a robust control allocator and an online actuator effectiveness estimator. Firstly, the backstepping control law is developed for the strict feedback form of an Aero-Data Model in Research Environment aircraft to produce the desired commands. Furthermore, a novel robust optimisation-based control allocation algorithm is proposed to distribute the commands among redundant actuators with the consideration of control effectiveness uncertainties. Lastly, the control effectiveness factors are introduced to denote the healthiness of the actuators, and the least trimming squares-based estimator is designed for online estimation of the actuator effectiveness. With the proposed scheme, good tracking performance, robustness and reconfigurable capability are achieved. Evaluation of the overall system is accomplished by numerical simulation with various conditions, including adverse scenarios where actuator failures occur. The results show the effectiveness of the proposed scheme.