The most common method for standard low lying dino (not the aggressive invader kind) is simple repeated removal, they tend to exhaust the silicate or whatever food source is boosting them then they die off. peroxide will kill them but people usually opt for physical removal first. if you are going to have a barren tank with only rock and sand and water and dinos go ahead and squirt some peroxide on them to help out, it can't hurt. There is no known practical dose at 3% that could hurt your filtration bacteria for the dosages you'll be using.
so about the sandbed heres my idea tell me what you think.
I can't think of a situation, unless carefully planned and the tank stocked around real/true long term sandbed maintenance, where the sandbed of a reef aquarium is not one big giant diaper w slow buildup.
So if you disturb part of it, or overlay a clean linen on top

, its covering up diaper waste below lol
if you are taking a tank down that far...why not clean the whole sandbed out and start clean. its the last chance you'll ever get is how I see it. do nothing with a sandbed partially loaded with waste, but if you have a chance to really clean one in the absence of corals etc why not start square one!
you could remove the whole sandbed, rinse it in clean ro water and most of the bacteria will xfer right back over to the new tank sans detritus since the biofilms will be mostly present.
Im thinking your sandbed isn't holding something that we need, its holding something you couldn't get rid of while things were running.