Resolved.
New procedure apparently for App Service SSL auto-renewals.
App Service SSL purchased via Microsoft and issued via GoDaddy need to have a validation of the CSR now.
the issue is, GoDaddy send emails to hostmaster@, postmaster@, admin@, info@ so if you do not have those email accounts they either get lost or stuck in Quarantine.
Separate issue, GoDaddy were incorrectly issuing a validation link to a site that didn't have a valid SSL assigned to it.
changed from .cn to .com and the validation worked.
Unfortunately the support from both sides was lacking in customer focus, one put the phone down and the other said they would come back to me in 7 days