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Originally Posted by Corey Balint
...The tube was then hung and therefore would have the openings at two different heights. Both ends would be open to Atmospheric Pressure.
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There's the resolution to your dilemma. The upper end is at a lower pressure than the lower one. In a compressible fluid, continuity of velocity is not maintained when the pressure changes along its path. Mass flow might still be constant, but at lower pressure, the velocity must be faster to get the same number of molecules to pass in the same time.