There is more of an effect on the fllter with the second treatment so it is best to shut the pump and filter off for the second 1 hour treatment. The first will have got anything in the filter the first time. Are you seeing the nitrite spike with the first treatment? This is one of the reasons flukes are hard to get. The concentration to get the flukes is also hard on the filter. The more organics in the filer the more protected it will be from the MinnFinn.