@B_Snyman , Firstly, on Azure App Service, App Service Certificates purchased from Azure are issued by GoDaddy. Azure Apps Service handles the CSR on the backend during the certificate purchase process, so typically this is not needed for Azure App Service Certificates.
From within Azure Portal, double check the domain verification and sync:
Select the certificate in the App Service Certificates
page on the Azure Portal (verify the right certificate), then click Certificate Configuration
.
From the Certificate Configuration page select App Service Verification. Just click 'Verify' to finish this step. Click the Refresh button until the message Certificate is Domain Verified appears.
Once the renew operation is complete, click Sync
. See this document for more details.