And my problem, should anyone find this useful:
pyzor discover was correctly updating the servers file for the user account it was called from.
However I have a --homedir set for pyzor in local.cf and as this is not the same dir as the user file hence the failure to update.
Deleting/renaming the servers file in the --homedir and then running spamassasin in debug mode sees this copy of servers being updated correctly.
Alan