If I remember correctly, when you pulled the Master Sword, something was supposed to happen to the spiritual stones and they'd lose their power and turn translucent. I don't remember what you did to power them back up again, and then I think the Door of Time would reopen, allowing you to go back in time if needed. Some of these cutscenes still sort of exist in the game through the use of the debug menu. Although I'm not aware of the whole meeting with Sheik, if it still exists or not.