All SSL certificates issued for Azure App Service before March 31, 2017, will receive an email to re-verify their domain at the time of renewal. You'll get this email even if auto-renewal is enabled for your certificate. This is a result of a change in GoDaddy policy.
Please check your email and complete the one-time domain verification to continue to auto-renew the SSL certificate. Also, note that GoDaddy requires you to verify your domain once every three years. You'll receive an email once every three years for that.