A prognostic system makes it possible to anticipate loss of functionality before it occurs with sufficient lead time to take actions that mitigate the impact of this loss. We focus on the forms of mitigation within the flight vehicle that influence the operational dynamics but do not directly amend the mission plan. Thus, we focus upon the reconfiguration of the feedback control strategy for the flight system. The high degree of complexity in the design and dynamics of modern aircraft is typically handled using a hierarchical control scheme in which there are several levels of control at increasing levels of responsibility: the component level, the subsystem level, and the system level. Our reconfiguration strategy involves mitigating problems that are detected at the component level at both the level in which the fault is detected and higher levels as well. There are, thus, two subproblems to the reconfiguration: (a) an adaptive control problem at the lower level to extend component life and derive new component performance limits, and (b) a supervisory control problem at the higher level to adapt the system controller to maximize system capability while respecting the performance limitations. Since our reconfiguration occurs in the context of a dynamic system, we need to respect the stability implications of the reconfiguration. To address this, we apply bandwidth analyses at the component level and the systems level in a robust performance context. A conservative criterion for stability is to impose rate limits for reconfiguration that insure that undesired, and possibly unmodeled, modes of behavior are not driven by reconfiguration activities. For specific hardware, extensions beyond this conservative approach may be warranted (e.g. to catch faulty behavior) and validated on a case-by-case basis, essentially by extending the component modeling to include a model of behavior under certain types of reconfiguration.