I don't see the Op mentioning a loss of run 'flooring'....
....but......
they will pack down the dirt in the run, they will also scratch it out of the run and they can dig prodigious holes, almost think I need apron on the inside of the run walls too and actually have some in parts of the run...
'Clean' sand, without dust...lol.
Sorry, but a lot of sand that you buy, especially in bulk, has 'dirt' particles in it that can become airborne(ie:dust).
I spent a lot of time researching sand when doing concrete sculpture and the cleanest sand I found was Quikrete brand Fine Sand. It is...