Update your API
We never heard why, but for some reason, Magento dropped a few APIs related to managing shipment and payment methods. We still have a few requests on Github pending, but in the meanwhile, we decided that we better write a bit of code ourselves. So, in order to sync shipment and payment methods, be sure to install the NcApi as part of your NAVcommerce Magento 2 extension.
Once your API is running fine, synchronizing is really easy. Just go to Departments/NAVcommerce/Administration/Sales/Shipment Methods and click Update From Magento. All the shipment methods you have configured in Magento will automatically appear in the list, and you can complete the configuration by selecting the right G/L Account and the corresponding NAV Shipment Method/Agent/Agent Service.