Just to let you know, almost nothing done upstairs will affect downstairs so you can close your doors and windows (hell, I can’t even recall if that would help if the cloud was upstairs.)
Z-levels might as well be separate, non-intersecting dimensions you can portal to with the use of stairs (and occasionally traps.) There’s the odd clever exception like monsters following you down a flight of stairs ,but that’s just a range/line of sight check with a timer attached after you make it down as I recall.
In short, for the cloud to clear you have to be downstairs and waiting as the reality bubble is more like a flat circle and doesn’t extend upward or down.