Theory: The mine was covered when the house was built. The internal support rooted away collapsed the covering earth of the mine. The moisture rising from the 40 foot hole, which would have had water in it, rotted the floor joists in that part of the room of the house.
Very plausible theory. Probably what happened.
I can't imagine not filling the hole up though. Those of us who are fortunate enough to live in the boondocks know the value of a good place to dump stuff.
I'd love to have a 40-foot deep mineshaft to use in my efforts to leave as complete an archaeological record as possible of my presence at the junction of the 20th and 21st Centuries!