In a previous paper we showed the effects of applying the Divided Exhaust Period (DEP) concept on two heavy-duty diesel engines, with and without Exhaust Gas Recirculation (EGR). Main findings were improved fuel consumption due to increased pumping work, improved boost control and reduced residual gas content. However, some limitations to the concept were discovered. In the case of high rates of short route EGR, it was apparent that deducting the EGR flow from the turbine manifold impaired optimal valve timing strategies. Furthermore, for both of the studied engines it was clear that the size and ratio of blow-down to scavenging valve area is of paramount importance for engine fuel efficiency.In this paper, the DEP concept has been studied together with a long route EGR system. As expected it gave more freedom to valve timing strategies when driving pressure for EGR is no longer controlled with the valve timing, as in the short route case. However, when evaluating different combinations of intake, blow-down and scavenging valve area, the optimal relation proves to be strongly dependent on the current EGR system and EGR rates. Hence, for different engine setups the trade-off between total intake and total exhaust area needs to be re-evaluated for optimal engine fuel efficiency. This paper also presents general trends in how different valve timing strategies and EGR rates affect both pumping work and boost pressure.