the specific answer to your breaking/removing live rock (functioning filter surface area) is this based on searchable logged jobs:
you do not risk creating too few bacteria to handle your collective tank waste after a removal job, a thinning down job, as long as you're still using some common degree of live rock afterwards. It is not true that your reef tank's cycle is adapted to this current degree of bacteria, and to ramp down slowly is safer, that's not true at all but it's the common recommend in situations like yours.
the uncommon but completely safe method is to make your pairing down as planned: with the sensitive animals held and covered from jumping elsewhere. this is so that any released clouding during the work doesn't affect them
and we're rip cleaning the tank because preserving that clouding by letting it resettle does not help the tank, being in a state of total waste removed with hungry corals able to eat up a bunch of fresh new spot food is what preserves that tank. you have the ability to de-age that reef at the same time you're handling it in an aseptic manner to prevent detritus cloud upwelling; to rip clean the tank removes years of pent up waste and simply buys more years you can re pack new waste in it. you're reversing the bell curve in quality that aging reef tanks display
you're reducing the need to ever have to use antibiotics like cipro to stop rtn by rip cleaning an aging reef tank, to be free of waste and accumulated detritus does for a reef tank what a trip to the dentist does for a human mouth. if you're going to access the core filtration structure of the tank, it needs to be done in a thorough manner already documented to work well on tanks like this.
lack of surface area due to pairing down the scape is not the risk, the hidden risk is 100% any clouding that results from the access process or is left in the system to resettle afterwards.
make the system waste free for the total win, and years added to lifespan.