Intuit and QuickBooks are registered trademarks of Intuit Inc. used with permission.
This is the expected behavior in BQE CORE-QuickBooks Desktop integration. QuickBooks Desktop does not support linking a single or joint invoice to multiple projects or jobs. The joint invoices sync to the top-level customer or job only.
If you restructure your projects as phases under a main project in CORE, the joint invoices will sync to the main projects, which are recognized as customers in QuickBooks Desktop.