This article focuses on numerical simulations of the granular mixing process in a vertical cylindrical mixer with two opposed flat blades with a 45° rake angle. Computer simulations were performed by the discrete element method. The blending was examined for the blades' stirrer speeds in the range from 1.9 to 960 rpm and three different initial spatial configurations. The development of the concentration patterns and the evolution of phase interphase between different types of particles have shown that the homogenization process depends not only on the system's dynamics but also on the initial spatial distribution of particles. The dependence on the initial distribution is provided by involving primary and secondary flows in different time-scale in the homogenization process. This ability of the individual flows to engage in the mixing is granted by the mutual synergy between the direction of movements of particles located on the phase interface and the orientation of the phase interface. Because there is a significant difference between the intensity of primary and secondary flows in most cases, an improperly oriented phase interface will significantly slow down the entire rate of the homogenization process. On the other hand, during the mixing process, the phase interface expands and deforms, which gradually also allows the rest of the flows to get involved in the homogenization process. Based on the results, the basic rules have been identified for effective homogenization. As a mixing index, the relative surface of the phase interface was used. By comparing individual homogenization curves, it follows that the critical factor for the homogenization process is the centrifugal force. When it is in balance with other forces, it encourages homogenization. On the contrary, if it becomes the dominant force in the system, it causes a significant deformation of the surface, and its effect on the homogenization process is destructive.