Ok, this did my job. But, feel free to share any other ideas.
I don’t know if it is the right method, but it works like a charm ??
// WooCommerce PDF Invoices & Packing Slips
// Generate PDF after the order
use WPO\WC\PDF_Invoices\Compatibility\Order as WCX_Order;
if( class_exists( 'WooCommerce_PDF_Invoices' ) )
{
WCX_Order::update_meta_data( $order, '_wcpdf_invoice_number', 987 );
WCX_Order::update_meta_data( $order, '_wcpdf_formatted_invoice_number', 987 );
WCX_Order::update_meta_data( $order, '_wcpdf_invoice_date', date_i18n( get_option( 'date_format' ), strtotime( '2014-09-20' ) ) );
}