The nitrate test is a bear. Shake shake shake shake shake.
If I change water as often as suggested here (50% weekly), I get a 0 nitrate test reading too. If I do a little less (won't say how much because I'll get blasted as a bad fish momma) they come up to something between 0 and 5. I don't use anything else to remove nitrAte, I do have a small number of plants. My ammo and nitrite are always 0 ... It's when they creep up that you have disturbed the cycle.
Sometimes when my test results make me wonder I change the proportions. For instance, doing the nitrate test with 2.5 ml of water or twice as many drops.
I had LFS check too ... I brought tapwater and some from my tank that hadn't had a pwc in 9 days or a gravel vac for 3 weeks. He checked the tank water, and said "ok you did a good job supplementing the tapwater, now let's look at your dirty water." When I told him that was the dirty water he asked more about my routine and said I have a good thing going.
Not advocating less tank maintenance, my point is every tank has its own ecosystem and it's possible to have one that results in little to no nitrate.
So if your test kit is good, and your plants if you have them are healthy, and the fish are healthy ... No nothing you did should kill your bb colony so it's probably all good.