It doesn’t just stay in your stomach. Your stomach is not just some bag filled with stomach acid all the time, at least not if your body is working correctly. When you eat food, your stomach makes the acid to break down the food, then the whole mess moves on to your intestines. Then the stomach is more or less empty again until you eat again.
As for how does stomach acid not affect your stomach, well, it’s making the stuff, so it doesn’t get affected by it. Unless you have issues, like ulcers and such. Then the acid definitely does affect your stomach.
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