Replacing subtrate isn't always easy being it hold alit of nitrates however being crushed coral i would turn ur power heads off keep filter on and scoop it out with a cup get as much as you can but you can leave what you have around the rocks. It will help with cal .. are trying to go with sand? The influx of nitrates shouldn't be to bad on the damsels being how hardy they are... what type of corals do you have?