Setting up a new multiserver ISPConfig with 2 name servers. To be able to use DNSSEC I can not set second name server as mirror of the first. My old setup is using this mirroring setup. Can I migrate with Migration Toolkit to this new setup so name servers are no longer mirrors? Do I have to modify all zones with allow transfer and also notify?
You can migrate your old master nameserver to the new master nameserver, and change the allow transfer and also notify value to the IP of your new secondary nameserver. You could do this in the DB and then do a resync. You will have to add all the zones as secondary zone, but you could write a API script for this.