I may have misunderstood the order here but it seems like you may have done things a little backwards.
I have had the pleasure of moving house/switching tanks a few times and I learn from every one of them.
Personally, I would have got the rock in first and set it up how I wanted prior to adding any fish. Then I would have added the sand, let the tank clear, checked parameters and only then would I have started adding fish and corals. I can appreciate that some of the corals may have been encrusted to the live rock.
I doubt the corals would have liked the cloudy unsettled water, neither the fish for that matter. Plus the fact that (from what I understand) that you would have had your hands in the tank moving stuff around would have been pretty tough for livestock too.
It probably would have been a good idea to leave the fish out until the tank had settled and I think a couple of losses would have been saved. I have done this overnight, even a few days, in totes/buckets and every fish was fine.
You live and you learn.
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