The deacetylation process is a key step in the lignocellulosic biomass pretreatment process that currently is done in batch reactors. A flow-through diffuser type reactor is a promising approach to make the process more efficient and economically favorable. A washing step before deacetylation can further reduce chemical usage and increase the process efficiency. However, the highly compacted biomass particles can cause significant pressure-drop for fluid flow through the bed, which in the worst case can cause self-enhancing pressure-drop leading to reactor blocking. Detailed understanding of the fundamentals of flow through a compressible packed bed is necessary to scale up the washing and deacetylation process. This work closely examines the classical Kozeny Carman equation and proposes modifications to accurately predict the pressure-drop at different compaction states. Here, a compressible packed bed model is further developed based on the interaction between solid mechanics and fluid dynamics. Experimental measurements of water flow through a packed bed of corn stover show good agreement with the developed model. Corn stover washing process scale up simulations show that smaller reactor diameter, higher friction lining material, lower process throughput, and higher process temperature is favorable in stabilizing the bed from extensive compression when the bed height is fixed.