09-16-2006, 12:25 PM
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If you have substrate in your tank, then you should be fine cleaning out the whole filter. Just as long as you DO NOT DO a gravel cleaning at the same time. Nitrifying bacteria colonize filter media, decor, as well as the substrate, so if you disturb too many things, then it could lead to a mini-cycle.
What I normally do is clean out the filter and just lightly place the syphon over the subtrate to pick up the detritus. I don't dig into the substrate, which is what I normally do. The following week is when I go back into the routine of a good gravel cleaning.