The Hybrid Hydraulic-Electric Architecture (HHEA) has, in recent years, been proposed as an energy efficient alternative to conventional load-sensing architectures in mobile machines such as excavators and wheel-loaders. HHEA leverages the advantages of hydraulic power and electric power to eliminate throttling valves while also improving the energy and control performance of the system. The architecture utilizes a set of common pressure rails to provide a majority of power and and a small electric motor driven pump to modulate this power to meet the exact demand. Previous work has developed a computationally efficient Lagrange Multiplier approach for determining the optimal pressure rail selections that minimizes the energy losses in the system. The static model used considers only the energy use for each pressure rail selection but not the losses associated with the valves during the transition. This paper presents an approach to include the switching losses in the model and in the optimization procedure. To capture the switching losses, switching events between different rails and at various input and output flow rates were simulated with consideration of valve spool dynamics. A parameterized model that summarizes the losses is then obtained, allowing switching losses to be added to the previous energy analysis. The performance of the switching loss model was compared with reference data obtained from a high-fidelity simulation model. To incorporate the switching losses into optimal control algorithm, an efficient dynamic programming approach that prevents frequent switching is adopted in place of the Lagrange multiplier approach. The overall effect of switching losses on the energy consumption and optimal control decisions is presented. In general, switching losses contribute to about 9–10% of input energy.