I do have deep litter issues. Like I have stated. I have never deep littered and this is my first year. I have noticed it is keeping my floor damp. I have wood floors in the coop and now I worry about wood rot. Could I put sand on the bottom to prevent that? It just started when the weather got nice and the coop thawed out. All the talk of ammonia smells in corners had me digging out my corners and they are all damp wood under.
You can put down a pond liner or thick plastic liner. Go up the wall with it a few inches. This will keep the moisture from your DL getting to the wood. I had the same concern, my floors are wood also, this seems to work well.