Structural health monitoring has focused on the use of computational models to capture the effect of crack-like discontinuities on the behaviour of acoustic-ultrasonic signals. However, few models have taken into account the effect of geometric complexity in combination with residual stresses generated during the fatigue crack growth (FCG) process. In this study, a finite element analysis model of a C-channel type aeronautical structure is evaluated under a pitch-catch scenario. Three different finite element model configurations were considered in order to understand the effects that residual stresses of a fatigue crack emanating from a through-hole have on the guided Lamb wave propagation behaviour. The results demonstrate that numerical modelling is able to capture the change in amplitude and the effect of a phase shift on the guided Lamb wave behaviour due to the presence of the discontinuity and the stress field generated during the FCG process.