If your rinsing the filter material with tap water you might kill the bacteria rather quickly with the chlorine, even if you are adding treatment to it later, the damage could already be done. This is only my assumption, any else verify this?
If you need to clean your filter material and its either really dirty or your lazy (both which would describe me lol) then if you have 2 filters going you can thoroughly rinse 1 without too much worry about killing off the bacteria since your other will still be working - as long as both filters are about equal capacity. Thats one nice thing about having dual filters. If you have seperate bio media and filter pads, you can similarly rinse the pads really good in tap water but dont rinse the bio media - just let it be if its not too bad. The filter pads may have some bacteria in them but if you have a good volume of bio media it shouldnt be a big deal rinsing just the mechincal filter pads. There is also bacteria on most surfaces in your tank - mostly in the gravel. if you have a bare-bottom tank I suppose there is a lot higher demand on the bacteria in the filter in which case you have to be more carefull.
