When you have a stomach virus and it causes extreme bowel movements to the point of almost pure stomach acid, does this kill off the bacteria in our intestinal tracks?
No, since the pH and the conditions are different in the different compartments (stomach, small intestine, colon) of the bowel. See this figure (taken from this website) for the differences:
There are not that much bacteria in the stomach, so even even nothing else than acidic stuff comes out, the bacteria are not affected. And even when you have a severe diarrhea, there are still enough bacteria left to keep it colonized.