I switched from puka to aragonite sand last june.
I was sucking out a ton of stuff from the substrate when vacuming during water changes and had pretty high nitrates... the problem with that stuff is your clean up crew can't get at the stuff before it gets into the substrate
As long as you have alot of biomedia (rock, biowheel, bioballs, etc) don't sweat swapping out too much-- realize all the stuff you are pulling out is decomposing and conributing to your bioload....so by removing it with your substrate (which also handles part of your bioload) you are removing a large ammonia source..
When I pulled mine out I had rock, a biowheels, and bioballs (yes I was bad back then).
Here is what I did on my 72-- I made up about 20 gallons of new water in a tote. I set up 3 other empty totes--- I siphoned into one of these-- moved most of my rock into this. Siphoned more into a 2nd one (put my fish in this one), moved heaters, and powerheads to these totes--
In the third tote I siphoned/vacuumed my substrate into-- this water was pretty nasty.... this was to harvest bristle worms and some pods from my old tank..
Scooped out the old sustrate with a plastic dustpan, wet vacuumed the bottom of my tank to get out the rest of the gunk and shells.... poured my sand in (did not rinse) and spread out--- put a couple of pieces of base rock in the bottom of the tank-- pumped the water from the totes back to the tank so that it hit the base rock and ran off into the sand (this minimized my sand storm)-- added rock as the water got deep enough--- added fish after I arranged all the rock the way I wanted-- topped off tank and started everything back up...
When I was done, I dug throught the gunk in my vacuumed to tote and picked about 50-70 worms and some pods and put those back in my tank to help seed my sand.
I fed lightly for a few weeks to be safe but had no detectable ammonia spike and everybody came through fine. THe water was a little cloudy the rest of that day but was clear by the next morning.