A general two tier framework for vehicle health monitoring of Guidance Navigation and Control (GN&C) system actuators, effectors, and propulsion devices is presented. In this context, a top level monitor that estimates jet thrust is designed for the Space Shuttle Reaction Control System (RCS) during the reentry phase of flight. Issues of importance for the use of estimation technologies in vehicle health monitoring are investigated and quantified for the Shuttle RCS demonstration application. These issues include rate of convergence, robustness to unmodeled dynamics, sensor quality, sensor data rates, and information recording objectives. Closed loop simulations indicate that a Kalman filter design is sensitive to modeling error and robust estimators may reduce this sensitivity. Jet plume interaction with the aerodynamic flowfield is shown to be a significant effect adversely impacting the ability to accurately estimate thrust.