The atmospheric boundary layer (ABL) flow over a smooth-to-rough surface heterogeneity is studied using large eddy simulation (LES). Two wall models are evaluated which prescribe the wall shear stress at any instant of time as a function of the velocity field at the first grid point away from the wall. The first Bouzeid (BZ) model locally applies the similarity theory using the twice-filtered velocity field. The second Abkar (APA) model blends the upstream and downstream profiles with a blending function. The wall shear stress is very sensitive to the wall models used, whereas the other flow statistics such as mean streamwise velocity, total shear stress (TSS) and turbulence intensity (TI) are insensitive. The LES data for these flow statistics agrees with the experiments up to a certain downstream distance behind the surface roughness jump. The internal boundary layer (IBL) heights obtained from the TSS or TI profiles in the experiment are much higher than those obtained from the LES. This suggests that the IBL relation that is given as an input in the APA model should be modified to match the experiment.