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But the cyanobacteria will take time to work. What about the thousands of years in the meantime?
I wouldn't want to build a city that I know will fall to its doom at some nebulous point in the future.
If it takes thousands of years, monitoring air density can probably give you at least a couple centuries heads-up, like "we expect in 150 years from now that the atmosphere will thin to the point our cities lose buoyancy. That gives us approximately five generations to think of a solution."
The solution would be to evacuate back to Earth, because the surface still would be hostile to human life. Or don't waste the resources, and have some patience.
Or move the cloud cities to one of the gas giants (presumably where the water is coming from anyway, or at least one of their moons, so the interplanetary transport infrastructure would already exist at this point.