Most corals can handle significant amounts of time out of water. Walking/snorkling the beach in Hawaii personally confirms this -- many corals are exposed to the air/sun for HOURS each day.
I would just make sure you have the make-up water ready, and then just do it.
IMPORTANT though, is not to disturb your sandbed - since anything in there would get stirred up.
Regarding the deep sand bed releasing nutrients, this is likely the case also. There are many thoughts on the matter, but personally I prefer a shallow sandbed (1-1.5"), which I then have a sleeper goby to constantly stir it up to keep things clean and nutrient-free. If you are interested in removing/cleaning your sand -- I would recommend doing it SLOWLY so not to disturb it too much and release many nutrients too quick. Say remove a cup every few days/etc. If you do it gradually enough, you should not have an issue.
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Single System Setup: 210G SPS reef, 225G FOWLR, 72G water change, 50G frag, 120G sump. I promise a journal at some point! (anyone need some coral frags? I likely always have stuff that is frag-ready)
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