Hello; Another way is to siphon the fine gravel or sand into a bucket during a water change. The gravel/sand can be rinsed with a hose and the detritus flushed away.
Some things that make this less of a problem; I keep some cleaned gravel on hand to replace the amount siphoned out. With a few episodes the amounts involved can be worked out.
I do not try to do the entire volume of substrate at one water change. I work different areas of a tank at each water change. Doing a partial volume also has not had a negative effect on the overall amount of beneficial bacteria (bb) in the substrate.