If this is an FO
tank, then rinsing the floss in removed tank water would best preserve the bacteria in the floss. If an FOWLR
or reef tank, I would suggest ridding yourself of any floss/sponge materials completely. It is not really needed and the LR
will take care of your bacterial filtration much more efficiently without the fuss and muss that comes with keeping the canister clean.
If the floss is essential, when it comes time to replace it there is not really much you can do except swap out the old for the new. If you have multiple media trays or a housing for carbon, then only replace one item at a time. This will cause less of an impact and allow nitrifying bacteria to colonize the new media faster.