Had a wonderful summer in the St. Louis, MO (USA) area and a productive honey harvest. I love my Flow Hive and harvesting honey is a joy compared to the conventional method, which is so destructive to the bees and their hive. Now that the honey is harvested, it’s time to turn my attention to varroa mite treatment. My hive is comprised of a brood box (bottom) and a deep for the bees winter stores of honey (middle), with the Flow Hive for my honey on top. Question - should I remove my Flow Hive, which I use as a honey super, during treatment? I will be using Apiguard, which seems to be effective, but concerned that the Apiguard could penetrate the plastic of the Flow Hive frames somehow. Would appreciate any feedback or opinions regarding varroa treatment with Flow Hive on or off, please.
Check out the very good article by Randy Oliver about late season varroa treatments. You can read the details or look at “Figure 6”. He places the Apiguard on top of a double deep brood hive, no super (Flow), and adds a 1.5" spacer.
http://scientificbeekeeping.com/a-test-of-late-summer-varroa-treatments/
Hope that helps!
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I agree with Tim (@tjsutton), take the super off first. 
Now is the perfect time to treat, but you may need to repeat with a different treatment in late September or October/November if you have a heavy mite load.
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