whew...that was a long read. After a long day at work, I don't think I have an idea of your sump set up but here are my comments about your questions....
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Originally Posted by asylumdown
Does anyone have any input, advice, or sees an issue I haven't thought of? Should I take the reactor with GFO that's currently in the water change chamber offline for this, or should I leave it running in the hypo treatment? What about my biopellet reactor? Currently it draws and returns water from the skimmer chamber, but sits in the water change chamber, both of which will be in hypo for 8 weeks. Will the bacteria in it survive the treatment (and help maintain water quality in the quarantine system) or would I be better off moving it's inputs and outputs so that it's still part of the display system?
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You don't need GFO, biopellets in your treatment area. Those things deal with nitrate and phosphate which are not harmful to fish unless they are at a very, very high level. I would take them out.
Also get some ammonia badges and prime (or any ammonia binding agents).
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Originally Posted by asylumdown
Also, anyone have any advice on how to get 16 fish out of a 250 gallon tank in less than 2 hours?
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Borrow, steal...a lot of brute trash cans for water change/storage from your fish friends. Drain your tank and get the fish out.
Good luck.