The complex shock wave-boundary layer interactions are still a major obstacle in the accurate prediction and control of scramjet inlet/isolator flows. Moreover, the nature of interactions strongly depends on the state of the incoming boundary layer which may be relaminarized due to supersonic expansion near the ramp shoulder. While shock-turbulence interactions result in Reynolds stress anisotropy and turbulence amplification, relaminarization is characterized by the ‘freezing’ of Reynolds stress in outer layers. Such scenarios are typically outside the range of applicability of eddy viscosity-based models and may result in significant discrepancies in predictions of separation and aerothermal characteristics. This work focuses on a scramjet inlet/isolator flow, where the boundary layer passes through the expansion corner and shocks in close proximity. For this flow, significant discrepancies in the prediction of separation region and separation shock characteristics were observed with both the SST \(k\text{- }\omega \) model and the Reynolds stress model (RSM). By investigating the flow behavior near the expansion corner, we find that the main cause of the inconsistency is the strong relaminarization of the boundary layer prior to shocks. This was confirmed by examining some characteristic behavior of relaminarization such as quick decay in turbulence levels in the relaminarizing region, stress-freezing in the relaminarized region, deviation from the law of the wall, and value of the pressure gradient parameter exceeding the threshold value for typical relaminarizing flows. The models show some ability to predict the turbulence decay in this region, however, the discrepancy may be due to incorrect estimation of the eddy viscosity level and treatment of shock-relaminarized boundary layer interactions. Current observations suggest that a calibration of the turbulence models is necessary where expansion and shock are present in close proximity.