I agree with the others. Take out a couple cups of sand at a clip and accompany that with a water change to clean out what you'd be mixing up into the water column.
Another thing to mention is you may have another option if you want to keep the sand, but are just sick of dealing with it getting blown around. I had a similar situation recently because I made the mistake of using Bahamas Oolite sand, which is very very small grained. It was impossible for me to have enough flow for SPS going through all of my tank and not blow it all over the place. My solution for a bit was to blow my flow into the rock work, but I had a few dead spots and you could really tell it wasn't cutting it. What I ended up doing was adding about a half inch of thicker grade reef sand on top of it and I've been fine ever since. I was able to reposition my Vortech where I really wanted it and up the flow significantly without any sand storms. One thing to point out if you do go this route, it's important to really make sure your current sand is clean and detritus free or else you'll cap nitrates in when adding the new sand and creating a nitrogen pocket that could be disturbed later. Just figured this was worth mentioning.