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It goes up......
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As a non-cave diver, I'll take a layman's approach to this.
Depending on the materials that comprise the cave walls, the gasses will rise and slowly filter upwards through natural fissures--some extremely small--in the rock. After all, didn't the water have to get there, in some cases in a similar manner?
Like I said--a layman's approach to the problem. Feel free to correct or expand on this.
That doesn't seem satisfying, water doesn't leak through rock walls at any appreciable rate and It seems like some of these caves could be made out of solid rock. But I honestly don't know so I'll take your word on it.
Still curious about how long it takes for the air pockets to go away though. Days? Months?