Flight simulation is an important tool for investigating the impact of a wake-vortex flow field on aircraft response and on the severity of wake vortex encounters as it allows to evaluate a huge variety of encounter parameters under controlled conditions without risk, at low costs and time-efficient. The majority of simulation studies has used a pair of counter-rotating straight vortices to represent the vortex wakes. However, as part of the decay process, the vortices develop a periodic long-wave deformation due to Crow instability that may lead to a breakup into vortex rings. The paper describes a methodology to perform Monte-Carlo simulations of aircraft encounters with such perturbed vortices. A high-fidelity six degree-of-freedom aircraft simulation is coupled with a wake encounter simulation that includes models of wavy vortices and vortex rings, that are fitted to wake shapes from pre-computed large-eddy simulations. Application of the methodology is demonstrated by assessing aircraft bank angle upsets from encounters with straight and deformed vortices for different test setups. First results indicate that the impact of wake deformation is strongly affected by the simulated encounter scenario. For a full-scale Monte-Carlo simulation with uniform parameter distributions and assuming the same and constant vortex strength, vortex rings exhibit a lower probability of experiencing bank angle upsets above a specific threshold, whereas only small differences between straight and wavy vortices are observed.