Just to clarify something a bit -- and something which I have questions on myself and will begin a new thread regarding it in the Equipment/Hardware section -- with SOME filters, such as the Aqueon QuietFlow line which I personally use (along with an AquaClear 110), there are some parts of the filter which are supposed to "grow" and "house" the bacteria OUTSIDE of the actual pads, which is why some manufacturers such as Aqueon say you can toss the old, used pads and replace them...
In other words, with these Aqueons I speak of, you could, if you wanted to, toss the cartridges that actually catch the debris without fear of destroying the BB colony because the bacteria, on these specific filters, grow on "other parts" such as the "diffuser grid" and "cartridge holders"...here's some interesting information on how these work:
Aqueon Videos
Aqueon Videos