Unless you have an under gravel filter, there is only a very minute amount of bacteria in the substrate so vacuuming won't harm it. You need to get the waste out that is decaying and creating ammonia. As I mentioned, your nitrite is way above 5 ppm so you need to quickly get it down. I would do 50% water changes 2 or 3 times a day until you get it to at least on your chart and preferably down to .25ppm or less. Then change to 25% WCs as needed to keep it there. What is your nitrate reading? If it is high, it means that at least there are bacteria trying to process the nitrite but the level is just to high for them to catch up.