Sand will *mostly* go thru them, it's the few pieces that attach themselves to the intestinal walls that you have to worry about. Imagine a clogged artery ... it's the same thing but with the GI tract. A clogged artery doesn't happen overnight. If a beardie's GI tract gets plugged up you better get it unplugged quick (surgery) or the beardie will die a very painful death. And usually by the time any symptoms show up that the beardie is ill, it's already too late. Feces back up in the system and poison the body, then organ failure occurs. (This is how my vet explained it to me.)
And no, beardies don't spend even 25% of their time in the wild on sand. Australia is covered with many ground coverings. Beardies are usually perched up high on fence posts, rocks, and even found clinging to trees.
This is just my opinion. I'd get rid of the sand if it was my beardie. Best of luck to you.
Veronica
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Beautiful Dragons