GHA gong through Gills

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so I'm starting to get some more GHA from overfeeding. last time I manually finger pinched off what I could and did a water change then changed the floss after the GHA still in suspension filtered out which took a while. Many people use tooth brushes to remove it. my question is how harmful is it to have all that flow through fish gills? My gha is mostly on the lower rocks so removing to brush outside the tank will really mix up the nutrient levels etc..since I need to re-adjust everything. even doing one rock outside at a time I'd have to remove a bunch. I also have micro brittle stars inside the rocks so not sure how removing to do a curb and putting back would do?
 
I wouldn't worry about the fish, should be fine. For removing rocks to clean them, just give them a good shake before removing it to dislodge any of your hidden cleanup crew.
 

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