Jumping in- the way I see it- Depending on what you have in your tank, the size and age of your tank, and your rock work- you would probably take everything out, put it in a big Rubbermaid with your water, heat, and flow- change out the substrate and put everything back. It sounds simple (doesn’t everything at first in this hobby?!) but it may cost you some corals, stress the fish, diminish your beneficial bacteria and cause die off, begin territory wars, generate algae blooms, nitrate and/or ammonia spikes as all that settled detritus is unleashed and the good stuff removed, set off a new cycle which could cause more losses etc... what is your tank stocked with? If you leave everything in and try to remove the substrate either all at once or in thirds around your existing structure- depending on the stability of your structure and how picky you are about how much gravel you leave behind- you risk fish stress, scratching/cracking glass, rock slides, and the nutrient spikes etc. There are always risks when you mess with your tank and usually it goes... mostly okay-ish. It will be frustrating as heck and you will likely run into one or two issues at least as described above so just mentally prepare for that. I think that’s why the other poster indicated that copepods shouldnt be your main concern. Restructuring the bedrock of an ecosystem isn’t usually quick or easy- especially if you are dealing with an established reef set up. if it’s a small tank it will probably be a lot more manageable as far as physically getting it done than a large one. Will you be using dry sand, live sand from like an lfs or bagged “live” sand like from the pet store?