Unfortunately this isn't a feature of SQL Dependency Tracker.
Finding invalid objects is going to be a feature of SQL Prompt 5, which will be out sometime this summer. I can put you on the beta notification list if you like, which means you'll be able to try an early version of the functionality.
In the meantime, you'll have to do what you're doing. If you try to use SQL Compare (or SQL Packager) to deploy your schema to an empty database, it will fail due to these invalid objects. You can then fix them one by one. It's not ideal, but until we've added this feature to SQL Prompt, it's the best I can think of.
Red Gate Software