I'm having this issue too.
I've switched off iCloud synching for an app, on all devices and deleted the app.
If I search for a file that I know was in the folder, it shows up and the path bar shows it in the app's folder on iCloud Drive. However the folder is not visible. Trying to move back up the filepath, via the Path Bar doesn't work. I simply see the base level of the iCloud Drive, with all the other folders, but not the one that has gone 'invisible'.
Shift-Cmd-. isn't working for me either.
Does anyone know how I can make all folders visible on the iCloud Drive?
Ventura 13.2