we have a thread for that here
http://reef2reef.com/threads/the-of...ead-aka-one-against-many.230281/#post-2681445
reef surgery is great science, much is on the line. like a real thoracic dive, can be done consistently if you follow the right order and use the right tools but to act partially might be death depending on how stored up the system is. cleaning it out wont kill the system, but mixing in half rotten waste among sensitive animals sure can.
-depending on how bad the rock has retained detritus, after you scrub the outsides of algae (if applicable) you unplug them (which improves filtration) and begin an outflow of detritus that if left in a white bucket, will show as actual waste pellets this needs to be accounted for. if you stuff those rocks in a bucket with a bunch of fish, and all this waste, you get a mini cycle
-the cycle or mini cycle name (cycles are rarely low level prolonged, they are usually short and eventful among tanks of live rock) follows detritus.
leaving detritus in unpredicted places and then moving it is your major risk, with a pic here we could easily see whats up
don't store fish in containers with rocks for the reasons above, we found in one such tank cleaning (it always relates back to detritus somehow)
keep helping points- bacteria is of no concern in the process. not during rinsing of your new sand, or rinsing off rocks, none of this stops your filtration
preserving micro life to avoid dieoff isn't hard, those tend to house in the live rock so we clean it carefully
in most cases there really isn't any hidden waste, its all in the sandbed that would fail a drop test horribly (anyone should be able to grab sand and drop it down in the tank cloudless, if their export animals/systems are working...detritus has no place in the tank unless out of sight out of mind is the selected mode, with constant offsets like carbon dosing or nitrate/po4 detailing etc