The Abandoned Dungeon Entrance has also been sealed - meaning the only way to progress is from Lord Kuro’s room, as the Upper Tower has also been closed.
Thankfully you can still upgrade your own Shinobi Prosthetic on your own - and you should absolutely be sure to get one of the Lazulite upgrades, as well as Suzaku’s Lotus Umbrella - for reasons we’ll explain soon. Even worse, if you take the Shinobi Shortcut door to the Dilapidated Temple, you’ll find that the Sculptor has left for mysterious reasons, and the branch grapple points leading to the Outskirts have been obliterated. Things will be very different in Ashina now - far more than the changes that happened at dusk.
Speak to her to learn what’s going on, and Emma will give you the Secret Passage Key, which can unlock the door back to where you first tried to escape with Lord Kuro and were cut down by Genichiro.
Returning to Lord Kuro’s Room, you’ll find the young lord has disappeared, and in his place is Emma and a fallen Isshin Ashina. Video Guide: Ashina Castle (Night) Castle Grounds