Mine all dig down into our run too, but I encourage them to mix in the native soil below, with all the wood chips and organics I've put into the run - now several years later it's like a giant compost pile and I can pull out some fantastic soil that's a nice blend of organics and mineral based dirt. I used to have gravel/rock all around the perimeter of my coop before building the 2nd run around everything and all those rocks have since blended in with the goods, they're a non-issue, aggregates are good in soil mixesI have at least one chicken who likes to dig dust baths almost to the core of the earth.
Ok maybe not that deep but I've seen holes deep enough that all you can see is her head poking out. Since my run is built on a gravel base, I'm trying to prevent the gravel from being dug up and mixed in.
The wood chip pile had aged 6 months before initial use in the run. Currently the pile is about a year and a half old. So definitely not fresh.