I have never used any of the cycle jump start products, so I am not sure where the beneficial bacteria live when you do, although I would think they would colonize on the filter media. Any who, when cleaning your filter your should almost never clean the bio media (either the sponge thing or the ceramic pieces depending on the style of filter you have). As for the mechanical filter, if you have only one in your filter, then just switch it around in either old tank water of clean dechlorinated water. If you have carbon, I would ditch it as it loses it's effectiveness after 2-3 weeks at best. You can add more bio media in it's place.