The reason you allow all those levels to spike is because that's what is going to happen. It's almost impossible to avoid, because you have some much material that is going to die, like sponges growing on the rock, and other things that just can't survive in a tank.
The spike in ammonia, followed later by the spike in nitrite is because the various groups of bacteria need to populate the rock, and consume the ammonia and nitrite. It's basic to getting the nitrogen cycle going.
Making water changes, while you are curing live rock only slows the process down. You just drag out the process and make it worse on anything that might survive. It's been my experience that you actually loose more when you drag out the process.
Yes it does help to remove obvious dead and dying material, but don't scrub the rock. You'll also remove a lot of wanted stuff.
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