Well, if we're gonna get specific about this, I think it would be reasonable to expect some decrease in atmospheric pressure for the simple fact that as the global sea level rises, the total surface area of the planet will increase also. Therefore you would have the constant atmospheric mass distributed over a larger volume and thus a decrease in pressure would result. Still, in order to make a meaningful comparison we'd need to know what the atmospheric pressure would be on the surface of the waters assuming they had risen 29,000 feet, and I know it wouldn't be equivalent to what a person experiences at 29,000 feet above today's sea level. I'm sure it's somewhat simply calculatable, but I don't know where to get the appropriate figures, nor do I care enough to be bothered.
The biggest problem is actually the *increased* (intensely increased) pressure before the water falls...
Well... I was sort of going along with Walt Brown's squirt-gun Earth model that puts all that water beneath the Earth's crust before the supposed flood, not suspended above the atmosphere.