Marxman187, post your ammonia, nitrite and nitrate levels when you acquire your test kits.
Out of curiousity, what size tank do you have and how many fish are in it and what is their general size?
One simple way to ensure the biological filtration will remain fully functional is redundant filtration (or 'overfiltration').
While generally it's highly recommended not to wash filter media in tap water, the overall effects of washing or rinsing filter media in chlorinated or chloramine-treated water depends on variables (primarily the amount of bacteria contained in the rinsed media and amount of bacteria contained elsewhere in the tank, total surface area of tank, substrate and decorations, level of chlorine/chloramine as well as exposure time).
These variables (as well as the ability for the bacteria in the tank to instantly compensate for the wiped out bacteria) will vary from tank to tank and instance to instance.