The paper deals with a dynamical system governing the motion of two point vortices embedded in the bottom layer of a two-layer rotating flow experiencing linear deformation and their influence on fluid particle advection. The linear deformation consists of shear and rotational components. If the deformation is stationary, the vortices can move periodically in a bounded region. The vortex periodic motion induces stirring patterns of passive fluid particles in the both layers. We focus our attention on the upper layer where the bottom-layer singular point vortices induce a regular velocity field with no singularities. In the upper layer, we determine a steady-state regime featuring no closed fluid particle trajectories associated with the vortex motion. Thus, in the upper layer, the flow's streamlines look like there is only external linear deformation and no vortices. In this case, fluid particles move along trajectories of almost regular elliptic shapes. However, the system dynamics changes drastically if the underlying vortices cease to be stationary and instead start moving periodically generating a nonstationary perturbation for the fluid particle advection. Then, we demonstrate that this steady-state regime transits to a perturbed state with a rich phase portrait structure featuring both periodic and chaotic fluid particle trajectories. Thus, the perturbed state clearly manifests the impact of the underlying vortex motion. An analysis, based on comparing the eigenfrequencies of the steady-state fluid particle rotation with the ones of the vortex rotation, is carried out, and parameters ensuring effective fluid particle stirring are determined. The process of separatrix reconnection of close stability islands leading to an enhanced chaotic region is reported and analyzed.