Are you doing a co-simulation or just one way FSI?
For the case you are running Fluent only you have to ensure that the flow accommodate itself to the inflow change by scrutinizing the convergence and letting the flow settle in. You might need to increase the number of iterations per time step, switch off convergence by residual and check the transient behavior of some key parameters at some control points /surface/lines in dependency of the iteration. The profile of that monitor has to reach a non-changing level towards the end of each transient/time step.
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