User is trying to do phased fixed fee billing while some of the phases are already billed 100%. The user wants to join those billed phases also to the invoice.
You can easily add a project or phase on an invoice by setting up a project rule 'Always show in Create Batch Invoice screen'. Besides that, you need to opt for joint billing wherein Core combines the phases of a project or multiple projects of a client into a single, consolidated invoice. Check the Core Help for details.
Other than that, Phased Invoice and Phased Invoice with Expenses invoice templates should work for you. There are many options available in Global Settings > Invoice Templates that can help you change the layout of the invoices as per your requirements. Check the Core Help for details.