You have only one cartrige in the filter? If you remove the cartrige, you can lose a lot of bacteria.
SO, the best way would to have two, and alternate. Or, another media to hold bacteria would also be a plus placed in your filter with floss wrapped around it.
But I had the extras in my whispers, so I would just chuck it when it overflowed, or was slow.
I wouldn't ever in my whisper clean the filters the same day I chucked the cartrige either. *thumbsupsmiley*