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 Commerce 365 Magento 2 extension.
Once your API is running fine, synchronizing is easy. Go to Sales Shipment Methods and click Update Shipment Methods. After this, all shipment methods configured in Magento will appear in the list, and you can complete the configuration by selecting the right G/L Account and the corresponding Business Central Shipment Method, Shipping Agent and Service Code.
Be sure to do this before you start to synchronize orders. Otherwise, you might bump into a message saying that you are using an unconfigured shipping method code.