Despite their low probability, faults and failures can occur in aircraft for various internal or external mechanisms. The control surfaces of an aircraft can become faulty due to various reasons; they can either become permanently jammed (due to hydraulic or mechanical problems) or temporarily stuck (due to blow-down limits). A blow-down limit is a phenomenon where the actuator surface become stuck temporarily due to aerodynamic constraints during a particular manoeuvre. Once the aerodynamic forces are restored to their normal values, the blow-down limit phase ends and the actuator surfaces move normally. In this paper a sliding mode fault tolerant controller and a control allocation scheme is proposed to deal with actuator jams and blow-down limit problems. The proposed scheme has an ability to distinguish between an actuator jam and a blow-down limit, and reallocates the control signal accordingly to recover the nominal performance. The proposed scheme has been implemented on the RECONFIGURE benchmark problem, which represents a high fidelity model of a generic civil aircraft. Good results have been obtained.