The longer you keep floss the less bacteria there will be, the bacteria need to get all they need from water which has to go through the floss and thus through the biofilm in which the bacteria live. But the longer floss has been in place the more clogged it gets. This reduces the flow though the floss nd this deprives that bacteria of what they need.
The bacteria will exist in the greatest numbers where they get the most of what what they need. They only other important consideration is that the places they live are out of direct light. This is why filters are not clear- they are made of tinted of solid colored materials.