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The natural scale separation in the restricted nonlinear (RNL) modelling approach is exploited to build upon recent studies, e.g., Wangsawijaya (2020), that have used scale separation to provide insight into mechanisms underlying secondary motions in turbulent flow over spanwise heterogeneous roughness. In the RNL decomposition the large-scale comprises the streamwise averaged mean and the small-scales are defined through a dynamical restriction that leads to computational tractability, while providing good agreement with salient flow features. In agreement with the experimental work, our results indicate that energy of the large-scales is amplified over the low roughness region due to the secondary flow. The small-scales are shown to play a dominant role in the Reynolds stresses responsible for generation of the secondary flow. Conditional averaging of the RNL mean field reveals stronger momentum pathways over low roughness regions experiencing downwash in instances that differ from the time-averaged trends. Further analysis of the large scale indicates that meandering of low speed streaks in the RNL flow is in response to secondary flow momentum mixing.