m0nk did a very good job of explaining it. The Biological filtration within the system will be on any surface, although rock and sand have a better ability to house this bacteria because they both have a lot more surface area than the flat surface of the tank bottom and walls have. The filter pads do hold on to some of this bacteria, so they do aid in the denitrifying process, but there is not nearly as much within the pads as there is in the sand and rock, so the loss should be minimal. This is why I alternate changing my two filter pads. I change one, then in two weeks I change the other. This will limit the loss and keep you from shocking the system, although it probably wouldn't matter if I did both at the same time. I hope with all of these responses you can get a good idea of what we are trying to explain. Good luck with your tank and happy reefing!