It's big job agreed. Since you are having to customize the job around practicality/time and resources then these brainstorms might be tank savers:
-nothing you do will affect bacteria. If it takes four days, the bacteria aren't the risk... Losing them isn't a factor here. Bacteria only need to be wet, they don't need feed or perfect temps and salinity here, so that frees up concerns to be allocated. Detritus, half rotten proteins that expose ammonia and metabolites to sensitive animals, is every bit of the concern.
-however you divide up the cleaning, keep sensitives away from clouding. Be creative, even your rocks have shakeable detritus in them. Moving em to hosting buckets is relocating cloud... until worked they'll cast off detritus and leave clear trails of it wherever they get moved to (which is why actual cleaning is required)
The space they were formally sitting in, in the tank, will cloud when they're lifted out. If for some reason you take a few days to work while corals are unlit, in heated buckets etc, then day one back in the cleaned tank isn't full production mode. It's slow ramp up, don't burn me with bright lights and perfect params and zero algae all the sudden mode. First several days in new tank are overcast reef week/slo ramp back and easy on whites, those bleach. Blue doesn't bleach, helps in transition.
-the sand rinse thread has examples galore of tank take downs, I'm sure a few were time-adjusted as well. You might catch unspoken details, planning details, in the bulk examples that save your tank. Check out any one of the before pictures, imagine what their tank would do predictively before we cleaned (or replaced) their whole sandbed at once-then check outcome. Develop predictability to some degree in your tank, wing it as little as possible by reading others trials and outcomes.
-why feel pressed to reuse sand immediately? You could just toss it, rinse no old sand. Go bare bottom till chart growback/compliance of the rocks. You could easily add rinsed new sand later. Delayed sand is an option
- taking a few days to hold items, kept separate but heated and circulated, isn't bad. It's holding detritus for extended days, make day 1 highest effort run focused on the rocks. They're your dependable filtration base, and to remove algae and chemically kill it at the same time restores porosity, restores pass through and around, and boosts filtration. Give rocks primo effort up front, the rest can wait. Why not toss that old bed?
Full water changes, if this reef isn't huge, is ideal it's not harmful. The temptation is to reuse waste water, or not evacuate detritus, if we can trust that bacteria are bulletproof and the mud is the danger, you can customize your take down cleaning as needed. Here's the work for pattern hunting coming up
The help in the following thread isn't my opinions it's the logged outcomes. I didn't get a ton of long term follow up, people reef their own ways in time. But we did get updates long enough to tell if things died or not, it's the #1 thing people want to report. We used a common order of operations in every case, and we used the before pics in every case to isolate sensitives away from detritus.
https://www.reef2reef.com/threads/the-official-sand-rinse-thread-aka-one-against-many.230281/page-12
The outstanding irony in that thread is the deeper cleans are safest, and the partial cleans are the riskiest. A few days time won't matter, how thorough you are in the end matters.
There's either clouding in the new tank or there's not, simple as that.
All details about sandbed cleaning with examples are found in this thread above
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