Problem description
If you find a DNS “zone transfer” zone [] always auto disappear after restart server or restart DNS service.

Parent domain:
Child domain: domain using zone transfer function replicated domain.

This issue may caused by duplicate record in in MicrosoftDNS container.

1. Checked AD Users and Computers MMC – you may found an AD zone under System -> MicrosoftDNS with the same name as the secondary zone(

2. Deleted it from AD.

3. Tested by restarting the DNS server service.

4. Found that we could now start the service without the secondary zone disappearing as before.