I just did a breakdown on a much smaller scale. I put the liverock in a tub, transplanted everything else into my sump and refugium, after shutting all the valves, saved most of my water and when I got down to the last few inches I scooped the sand I wanted to save then sucked all the grime out with a shope-vac. I rinsed the sand with some of the water I saved, added back the water and sand let things settle then put the livestock back and did a water change. I had no adverse effects but again this was a total of 40gal. Took me all day!