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The wake of wavy cylinder has been shown to exhibit bistability. Depending on the initial condition, the final state of the wake can either develop into a steady flow (state I), or periodic shedding (state II). In this paper, we perform direct numerical simulations to reveal the Reynolds number effects on these two wake states. With increasing Reynolds number, the steady vortical structures in state I wake sways back and forth in the spanwise direction, resulting in low-frequency fluctuations in drag forces, but not in lift. For state II, the increase in Reynolds number is associated with the emergence of another spectral peak in the lift coefficient. The secondary frequency is associated with highly three-dimensional vortical structures in the wake. For both states, the wakes transition to turblent flows at higher Reynolds numbers, with the development of small-scale vortices. We further study the streamwise gust flows over the wavy cylinder. The time-varying inflow velocity results in a wide range of instantaneous Reynolds number spanning from the absolutely unstable flow regime to the bistable regime. Depending on the period of the inflow velocity variation, the wake perturbations grown at the absolutely unstable flow regime can be damped out in state I wake, or grow large enough to trigger the transition state II, resulting in loss of flow control efficacy. The above analyses reveal novel flow physics of the bistable states at unexplored Reynolds numbers, and showcase the complex transition behavior between the two states in unsteady flows. The insights gained from this study improve the understanding of the wake dynamics of the wavy cylinder.