You should turn it off. It would take out the prazipro from the water and it would go nuts anyway. What i do is keep it running but take off the cup. So it helps aerate the water and to make sure that if there's any flukes in the skimmer it gets killed too. Of course i can do that since the skimmer is in a large sump.
When I last used Prazi-Pro, I kept the skimmer pump running, but took the collection cup up. That way, you get oxygenation and won't drop the pH, which is what happened to me when I totally turned off the skimmer.
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