Sonic boom minimization is a challenge faced by the aviation community to enable high-speed civilian aircraft flying supersonically over populated land. One of the concepts proposed to reduce sonic boom incorporates a high-flow secondary nacelle bypass, to enclose the engine and its protrusions, to divert the flow around a gearbox through a set of inlet and exit guide vanes. To assess the flow quality within the bypass, computational and experimental studies were conducted and the present study focuses on the computational portion using traditional RANS-based methods. Three levels of geometric complexity were considered - the full engine, the aft vane section, and one channel from the aft section - to evaluate the global and local flow characteristics and to evaluate the influence of different turbulence models on the flow solutions. The aft vane calculations were conducted in "clean" and "vaned" configurations which correspond to experimental models whose data were used for validation purposes. Comparisons between full engine and detailed single channel calculations show a weak dependence on the turbulence model used for the mean flow predictions as well as strong turbulence-shock interactions. The clean and vaned aft bypass section predictions exhibit reasonable agreement with the experimental data but show a stronger influence of the turbulence model on predictive accuracy due to a laminar-turbulent transition.