Though being involved in the survey effort in Sandy Hole in the 90s, I have never seen the drawn up product so it is a little difficult to be certain. My understanding is that the Stonehills development is an underground one rather like those at Bowers Quarry and Inmothsay Quarry. I think it is very unlikely that such development will be deep enough to directly threaten the passages of Sandy Hole which are almost at the base of the Limestone, as the quarry will be after he quality dimension stone much higher up. Certainly this is the case at Inmothsay (after having a guided tour of the workings a couple of years ago, I simply do not think it would be economic to quarry the poor quality cherty limestones deeper down). The potential threat however is that quarry waste could find its way into the passages of Sandy Hole by one of the many rifts in this area. Stone dust sludge from the cutting of dimension stone could easily make its way down these rifts and block the passages in Sandy Hole, which do run under the Stonehills area.
One way to monitor this would be to make regular trips into the far southern reaches of Sandy Hole to see what is happening - I won't be volunteering for that! Out of interest, when was the last time anyone went to the bitter end of Sandy Hole...