Flight testing has been the historical standard for determining aircraft airworthiness - however, increases in the cost of flight testing and the accuracy of inexpensive CFD promote certification by analysis to reduce or replace flight testing. A framework is introduced to predict the performance in the special case of a modification to an existing, previously certified aircraft. This framework uses a combination of existing flight test or high fidelity data of the original aircraft as well as lower fidelity data of the original and modified configurations. Two methods are presented which estimate the model form uncertainty of the modified configuration, which is then used to conduct non-deterministic simulations. The framework is applied to an example aircraft system with simulated flight test data to demonstrate the ability to predict the performance and associated uncertainty of modified aircraft configurations. However, it is important that the models and methods used are applicable and accurate throughout the intended use domain. The factors and limitations of the framework are explored to determine the range of applicability of the framework. The effects of these factors on the performance and uncertainty results are demonstrated using the example aircraft system. The framework is then applied to NASA's X-57 Maxwell and each of its modifications. The estimated performance and associated uncertainties are then compared to the airworthiness criteria to evaluate the potential of the framework as a component to the certification by analysis process.