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I would still not turn the skimmer off, IMO. It won't hurt anything if it runs as long as it cannot collect the medication and remove it in the cup. I've done this with success many times. Just my .02
Agreed... so long as the cup is removed and nothing is being skimmed out of the water (like the medication.) But if you want to just let it run over, for aeration purposes, no harm in doing that. Just be prepared for lots of microbubbles for a few days.