Simulation of aircraft wake-vortex encounters is regularly applied in the research toward revised aircraft separation minima. Most encounter flight simulation studies have used a pair of straight counter-rotating vortices. However, after being shed by the generating aircraft, the wake vortices begin to develop a growing deformation due to the long-wave Crow instability, especially under low-turbulent atmospheric conditions when vortices decay slowly. In this study, two methods for simulation of aircraft encounters with such perturbed wake vortices are described and compared. The first method uses a vortex simulation model, which is based on analytical models of the deformation that consider the large-scale vortex shapes. The second method applies vortex-velocity fields from high-fidelity largeeddy simulations. It offers the highest possible level of realism and is used as the reference. The resulting aircraft responses induced by wavy vortices and vortex rings are reproduced with good quality by the vortex simulation model. The comparison of both methods shows that the vortex simulation model captures the overall impact of vortex deformation on the aircraft upsets. It can be used for future safety assessments that require a large number of encounter simulations.