1. Urine isn't sterile unless they put a needle and extract it. Now with a stone, you are right - you can get a uti.
2. I'm sure your Urine was sterile because cs works. Especially since you drink lots of it and at a high concentration.
3. Because of point 1, it is more likely that your urine was free of bacteria, but got contaminated during collection.
4. When you think of ask all 4 points together, your conclusion that cs kills all bacteria but somehow spares lactobacillus, while likely, is highly improbable. Like 99.99% improbable.
5. But in the spirit of science, and to satisfy your curiosity and mine, I suggest a simple experiment. Take 1 tsp of yogurt and mix it with 3 tsp of your cs that you are taking. Let it sit for 15 minutes while you mix. Now take that and mix it with 1/4 cup of milk and see if you you have yogurt the next day. If you get more yogurt next morning, cs spared lactobacillus bacteria. If you're stuck with milk that is about to spoil, cs killed lactobacillus bacteria. As a control, you would do the same with a bacteria that you know cs kills. I dont know if you have access to it. But this isn't a clinical trial, just a home experiment, so I think we will get an answer one way or another.
Let me clarify - I think cs is awesome and powerful, but to think that it miraculously knows which bacteria is good for us and doesn't kill it - well that seems a little far fetched, but not impossible. I hope you do this experiment. And prove me wrong, because that means cs is even more awesome than I think.