Q:

Fun this TTLs and many records in PDNS

I got very strange issue for me.
I have powerdns server with potentially thousands of cname records. This records inserted to my DNS via mysql queries from network http service. This is a way how I give free jhon_doe.MYHOST.COM domains for my clients.
Of course I want to update DNS information as soon as possible - for any of newly created domains. And that happens - in few minutes, or even seconds domain could be accessed. 
But after some time that domains dissapearing. Some time after they reappearing. 
I found out, that my ttl setup was previously:
SOA record: 12 hours
CNAME records: 1 hour
And then also discovered, that my primary DNS cannot notify my secondary DNS about changes. (It can, but secondary doesn't understand notify messages by some unknown reason. My secondary is NSD server, which is not under my control).
So the question is: Could it be, that when hostname record expired for current DNS, client asks for name from my SECONDARY DNS, which does not have this record yet? Giving back to client answer NXDOMAIN? Or that's a kind of my fantasy and I shouldn't think that things going that way?

A:

Clients don't know what the primary or secondary is. They don't care. Each listed nameserver is authoritative. If a client gets an (empty/NXDOMAIN) answer for a query from one (picked randomly), it won't ask the other.
For large zones that have to be synced very often you should probably run your own setup, and sync the backend databases for you nameservers in a more efficient way than copying the complete zone on each update (as DNS AXFR does).

