If you want the parent project of your phased projects to be inaccessible for billing and only bill the project phases, you can set the Type for the parent project as Main in the Projects > General > Details screen. Such projects become grayed out in the Time Entries and Expense Entries screens. So you cannot log time and expense entries against them. This also implies that you cannot bill these projects and Core does not show them in the Create Batch Invoice screen. Check the Core Help for more on Main projects.
Note: Core does allow you to create manual invoices for Main projects.