The beneficial bacteria lives in the filter media, not the filter material such as activated charcoal bags.
HOB or "Hang On Bback" filters usually have a sponge and a filter bag. When changing the filter bag you do not change the sponge or 'media'. Only the little bag with the charcoal material is changed. That way, you do not lose the bacteria that ultimately conditions your water. If the water flow slows or barely flows, you take out the sponge media and rinse it in the water you remove from your tank when performing a
water change. Never rinse it in clean tap water or hot water as this will kill the bacteria and never wring it out. Just swish it around in the water and put it back in place
Same thing applies to the bio-wheel type filters. You change only the charcoal bag. The wheel shouldn't get clogged.
I'm not familiar with the canister types.