Yep, done it a few times, Siphon it out, dump the water back in, siphon some more until it's all gone.
As was already said I'd avoid crushed coral, my reasoning though is that crushed coral tends to leak phosphates which mean food for algae. I'd go with a course aragonite. I'd also avoid black substrate as it absorbs a lot of your light where natural/white will reflect a lot of light. It made a huge difference in my tank, I had the black and it looked sooooooooooooo dark and .. well unlit, I siphoned it out and put in natural and WOW everything looked so much better.
Doug
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