I ran into the exact same problem. I even set the quarry down to zero, and they just loop there while the stone pile stays at "pile is full".
i really appreciate you playing all the way through! you're probably the first person besides myself to beat the game.
for the new updates, you should be able to reload the page and the save should transfer over to the new versions.
if you're worried about losing progress, you can hit esc to open the pause menu and the "save a copy" will save your progress to your clipboard that you can then "load a save"
i will add save slots to the game though.