The den ("the well" for us crazy talkin' North Americans) is drained from the moment you enter the adult timeline. Nothing changes to reflect Link's actions.
The majority of the Spirit Temple cannot be explored by adult Link until child Link has already made alteration. We do not know what state it exists in when the adult timeline begins, and we do not know if Link can change its future by changing te past.
We'll come back to the Magic Beans, which are a key factor in this argument.

You mentioned the Wind Mill man; this rather interesting fellow teaches Link the Song of Storms in the adult timeline... but Link teaches him the song of storms in the Child Timline. Something we must determine here; who knew the song first? Where did it come from?