Reef flux & skimmer question

AngryMike2016

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Hi folks. I am about to begin a course of Reef Flux to treat a bryopsis outbreak in my Biocube 32. The instructions say to turn off the skimmer for the first 3 days.

Would it be okay to leave the skimmer running, but have the cup off? I'd like to do that for the oxygenation that the skimmer provides.
 

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