I work across multiple projects with Unity. On the larger projects this is super useful to find and get to files/folders you access often. The Favorites is a nice place to bookmark folders - fantastic feature - until you have to try to manage it.. then it falls short of functional. The favorites seems to be baked into the Unity app and not per project. Clicking on a favorite that isn't in your current project will ask you to delete the shortcut. The ability to organize the shortcuts is lacking. Started this thread to see if anyone else would like improvements here.
That makes sense, specially when you move your project, or even share with others. That why makes more sense, to have favorites per app, rather per project.