Filter to mark an order as not free if any of the items have a regular price (ie the order is only "free" because of coupons or discounts) for the WooCommerce Sequential Order Numbers plugin

gistfile1.php

add_filter( 'wc_sequential_order_numbers_is_free_order', 'wc_sequential_order_numbers_is_free_order', 10, 2 );

function wc_sequential_order_numbers_is_free_order( $is_free, $order_id ) {

	if ( $is_free ) {
		$order = new WC_Order( $order_id );

		// lets make sure the items truly are free, and not just on sale, or discounted with a coupon
		foreach ( $order->get_items() as $item ) {
			$product = $order->get_product_from_item( $item );
			if ( $product->regular_price > 0 ) return false;
		}
	}

	return $is_free;
}