Don't have a sump so I use the baster just before water change. This way the nasty stuff gets sucked out of the display with the siphon/vac thingy. I also jam the vac down into the substrate to stir things up.
If your procedure of stirring with the baster & simply making new piles hasn't caused your livestock to suffer ill effects, I guess you're ok. Skimmer will likely pull much of whatever you stir up eventually.
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