Chlorine can kill your bacteria pretty quickly. However, it won't be instantaneous and it won't kill all your bacteria. Unless you are doing a massive water change. If you are changing 10-20% of your water, the chlorine gets diluted very effectively by the water still in the tank. It would be an entirely seperate issue if you added over 50% of chlorinated water to your tank. Plus, any bacteria you do kill would be in the tank iteslf. There is still a huge colony active in the filter (unless for some reason you pour your water into the filter instead of into the tank). Some of your bacteria may die, but you shouldn't experience a massive die off (and therefore a mini-cycle) if you are changing up to about 20-30% of your water at a time.
That being said, I add my dechlor first, just due to an abundance of caution. Also, I might forget it otherwise. Very often, when I top off evaporation I do not dechlor the water first. As I am putting in so little the chemicals in the water will be sufficiently dilutted by the volum already in the tank.
\Dan