Board Thread:The Panopticon/@comment-25041817-20151128210342/@comment-5791028-20151129153452

It's explained in the episode that the castle resets itself every 82 minutes (i.e. the flowers being put back together). So presumably, the stool returns to its original position and the window repairs itself. The Doctor is not part of the castle, which is why his skull(s) remain behind.