In order to predict oscillating loads on a structure, time-linearized methods are fast enough to be routinely used in design and optimization steps of a turbomachine stage. In this work, frequency-domain time-linearized Navier-Stokes computations are proposed to predict the unsteady separated flow generated by an oscillating bump in a transonic nozzle. We also investigate the interaction of backward traveling pressure waves and moving surface on the unsteady behavior of a strong shock-wave with separated boundary-layer. This case is representative of transonic stall flutter of a compressor blade submitted to downstream stator potential effects. The influence of frequency is first investigated on a generic oscillating bump to identify the most unstable configuration. Introducing back pressure fluctuations, we then show that the aeroelastic stability of the system depends on the phase-shift between the fluctuations and the bump motion. Finally, we propose to actively control the instability by generating backward traveling pressure waves at prescribed amplitude, frequency and phase.