The dust that you might be speaking of could be built up detritus. Probably not actually dust from your crushed coral, as long as you rinsed it really well.
just out of curiosity, what are you parameters? I believe this would greatly determine wether or not you go moving things out of your system vs's vacuming the substrate. JMO
I ended up tearing the tank down and starting over due to ich, so I removed all the sand and cleaned the living **** out of it. Then only put half the amount back when I set the tank back up.