Strange thing...I downloaded the update on the itch.io desktop app, opened the game, started a brand new game, and yet it still ended at the same place it did before. When he spotted the doc in that hallway and panicked. I've confirmed I have the 1.1 version downloaded, but the "About" section of the game shows 1.0. No idea what's going on there. Going to try downloading the zip file and trying that way.
Viewing post in Cloud Cuckoo Land v 1.1 Out Now comments
When I had this with a different game, the problem was that the update created a new map instead of replacing the old one. Go to the place where you downloaded its files and check if that is the case. If it is, make sure to transfer any important files you created after installation (like screenshots and saves, although in this update that has become redundant) to the new map. Delete the old one or put it in a different map Itch won't check as a backup, and your game should work fine again. Tell me how it goes.