I've found that completely uninstalling and reinstalling the system extension allows us to provide a flow verdict for existing connections.
This is most likely because when installing a new system extension is temporarily causes network outage and requires all existing connections to attempt to reconnect. So in this case "existing" is a misnomer.
Uninstalling and re-installing is a no-go since it causes UI popups.
In my testing, it seems to only way to provide a verdict for existing connections is to force all existing connections to re-connect by forcing a network outage, thereby allowing us to place a verdict on these "new" connections.
Please can you confirm there is no better approach for allowing an NEFilter to provide a verdict on existing connections, when these connects are going down a VPN tunnel ?