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Corals are resilient. Are you afraid of messing with the Nitrogen Cycle? Maybe buy yourself one of those bacteria-in-a-bottle and dump it in the DT a couple days in advance before moving large amounts of rock. IMO, if you do a lot of changes the corals might not like it but they will rebound after 2-3 days unless something drastic happens.
Personally, if I do not like how something looks in the tank. I do it towards the end of my light schedule -- for example, my lights start to dim at 6pm and then completely shutoff at 9pm. Between that last 1 hour, all the coral polyps have retracted and makes moving the rock-work around is pretty simple.
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