yes , cleaning ur ' bacteria house' with tap water kill them. i am unsure whether is it due to chlorine or different salinity . but if there is a need to wash ur media, do wash it with slightly warm tank water to clear ur debris.
leaving ur water for days does dissipate chlorine into the atmosphere as chlorine is highly unstable. but there is this thing call chloramine which will never dissipate into the atmosphere.
once heard from my environmental prof saying that singapore do not use chloramine.. but i do not take chance, use water conditioner like seachem PRIME help to make the water condition better for water change