gistfile1.php

<?php
    $shipmentPackagesResponses = $verifyShipment->getPackages();
    $shipmentPackages = $shipment->shipment_packages;
    foreach($shipmentPackages as $key => &$shipmentPackage){
        $shipmentPackage = $shipmentPackage->toArray();
        $shipmentPackage['tracking_code'] = $shipmentPackagesResponses[$key]->getTrackingCode();
    }

    $shipment = $this->Shipments->patchEntity($shipment, ['shipment_packages' => $shipmentPackages], [
        'associated' => ['ShipmentPackages']
    ]);

    $this->Shipments->save($shipment, [
        'associated' => ['ShipmentPackages']
    ]);