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I'm asking if someone can verify if my DNS hosting idea is possible or has any flaws.

We would host our own primary DNS server for all zones and configure it to allow zone transfers to a set of IPs which will host the same data as secondary dns.

At my registrar for each domain, I'd like to set the NS records to only point at the secondary DNS servers because we don't want folks to rely on our primary server being available at all times.

Assuming the zone transfers have completed for the secondary nameservers already, will this plan work even though the primary DNS server is not listed in the zone for every domain?

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up vote 9 down vote accepted

Sure, this arrangement is commonly called "stealth master". For example, see the article Why you should use stealth master DNS.

The DNS system does not make a distinction between "primary" and "secondary" DNS servers. There are simply a bunch of NS records listed for each domain, their order or priority is not relevant (they are all presumed to contain the same data). How you arrange distributing the data amongst those NS servers is up to you.

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