This paper addresses the extended Kalman filtering approach to aircraft engine gas path analysis with control loop parameter uncertainty, which results from faulty sensors and actuators. A novel approach of gas path performance anomaly detection is proposed during the life course, which relies on combinations of recovered and actual measurements. A couple of adaptive onboard engine models (AOBEMs) are designed independently tuned to the real engine with state buffers, and sensor and actuator fault isolation (SAFI) logic is developed using hybrid matrices of the AOBEM couple. Neighborhood measurements with prior thermodynamic analysis reconstruct the faulty sensor signal once the control loop fault is recognized by the SAFI logic. The contribution of this paper is to develop engine performance monitoring against uncertain parameters over time in a control loop, and the gas path fault false alarm rate is independent of sensor and actuator faults. The tests involve abrupt fault and degradation datasets of the aircraft engine life cycle in the flight envelope, and the results demonstrate the superiority of the proposed methodology in the uncertain engine control loop.