Rules control how a project behaves or gets billed in Core. In case of phased projects, you should set the rules at the parent project level so that they are pushed to all the phases. You can then edit those rules at the phase level, if needed.
To ensure that all phases of a project show up on a phased invoice, irrespective of having un-billed, approved time and expenses associated with them, you need to turn on the rule 'Always show in Create Batch Invoice screen' in the Projects > General > Assignment screen. Check the Core Help for details.
Adding this rule allows you to include, for instance, completed and yet-to-start projects on a joint invoice. Or add all phases of a parent project to a phased invoice.