At the start of Chapter 12 you’re back upstairs. There is a notice to catch a Jewel Thief on the wall by the Gondola that you ride to the Clock Tower. The Merchant is asking you to track down a missing Scratched Emerald in the courtyard.
Head back to the courtyard and a crow will lead you west back towards the Merchant area that was by the Wine Cellar. The nest is on the roof just before that Merchant location. It’s not actually in the Courtyard. That’s just where you first see the crow.
The wall down from the Merchant holds two requests. This one and The Disgrace of the Salazar Family one.
The nest is just through the arched doorway.
