I've now replaced every "Power Net Portal" component with a standard "Net Portal" while keeping the designator VDD. This update should now have your VDD objects behave as standard Net Portals (i.e. not being excluded from BOM/PCB automatically).

Please refresh your project view or schematic to verify the changes. Let me know if you need any further modifications.

I've connected the VDD pin of LED1 to the Net Portal VDD. You should now see a net linking LED1 (VDD) to VDD throughout your schematic.

If you don't see the connection immediately, please try refreshing your schematic view.