AbstractA companion paper by Fritts et al. (2022), https://doi.org/10.1002/2021JD035990 describes the consequences of decreasing horizontal resolution in the description of mountain wave (MW) propagation, breaking, and large‐scale responses over the Southern Andes reaching into the mesosphere. This paper extends that analysis into the thermosphere, where MWs are confined below a critical level, but secondary gravity waves and acoustic waves become prominent and dominate the wave fields at higher altitudes. Like MWs at lower altitudes, the character and responses of secondary waves are strongly dependent on model resolution. MWs readily penetrate above a zonal wind minimum in the upper mesosphere and exhibit responses for varying resolution similar to those at lower altitudes. Both the MW and local mean responses weaken somewhat for resolution varying from 0.5 to 2 km, weaken more significantly for 4‐km resolution, and fail to approximate the high‐resolution results for 8‐km resolution. MW momentum fluxes and induced local mean responses are very different than those in the mesosphere, but exhibit similar variability with coarsening resolution. Secondary gravity waves at larger scales arise due to MW‐induced mean wind decelerations, hence are not highly sensitive to model resolutions of ∼0.5–2 km approximating MW breaking. However, acoustic waves are forced primarily by MW breaking, thus are poorly described at 2‐km resolution and absent at 4‐km resolution. These results reveal the dynamics that can and cannot be explicitly modeled as resolution is coarsened, and may aid in assessing, parameterizing, and/or compensating for the unresolved dynamics and their consequences.