Simulations of reacting multiphase flows tend to display an inhomogeneously distributed computational intensity over the spatial and temporal domains. The time-to-solution of chemical reaction rates can span multiple orders of magnitude due to the emergence of combustible kernels and thin turbulent reaction zones. Similarly, the time to solve the equation of state (EoS) for non-ideal fluid mixtures deviates substantially between the grid cells. These effects result in a performance profile that is unbalanced and rapidly changing for transient simulations, and therefore beyond the capabilities of traditional (quasi-)static mesh partitioning methods. We analyse this loss of parallel efficiency for large-eddy simulations of the ECN Spray-A benchmark with the multi-physics solver INCA and propose to mitigate the problem by introducing two independent repartitioning stages in addition to the classic domain decomposition for fluid transport: one for the EoS and one for chemical reactions. We explore various scalable repartitioning strategies in this context and observe that rebalancing computational load yields a significant speedup that is robust for various mesh resolutions and process numbers. The dynamic multistage load-balancing thus effectively removes obstacles towards good parallel scaling of INCA and similar solvers for reacting and/or multiphase flows.