Harry, so you have an enclosure filled with fluid and then you want to evacuate all the fluid and find out how it affects the walls? If so, I don't think Flow Simulation is going to work for you because you need to have one inlet and one outlet. (Or no inlets/outlets at all) You might be able to rig something up where you have your component in a larger environment and use the larger environment to pull from the smaller one but I think that is a real stretch.
If all you really care about is looking at the thickness of the wall (assuming stress/deflection), why not go straight to FEA and apply a pressure condition on the inside face of the model to simulate what you think is happening when you're pulling the fluid out? In the end, that will remove the step of having to run the flow and then transfer the BCs to FEA. (In Flow, the walls are rigid and they don't know what the pressure is doing to them)