An estimation of aerodynamic models of impaired aircraft using an innovative differential vortex-lattice method tightly coupled with extended Kalman filters is discussed. The proposed approach significantly reduces the order of the estimation problem by exploiting the prior knowledge about the undamaged aircraft and the detected information on the approximate location and extent of damage. Three different extended Kalman filter formulations are developed and their comparative analyses are performed through numerical simulations. Algorithms given in this paper can be used as the basis for online derivation of an aircraft performance model, which can then form the basis for designing safe landing guidance laws for damaged aircraft.