Issue after doing shell manual DNS zone update

- So we have a DNS cluster of 2 nameservers and the production server which is set to sync changes to the 2 nameservers. - We added NS3 and NS4 extra nameservers, and we added them to the cluster. Syncronized dns records, so NS1234 and prod1 server are all in sync. Problem: I made a script that would alter each DNS zone, and add ns3.domain.com and ns4.domain.com below ns2.domain.com for all dns zones (~450 dns zones.) Now, trying to use the "Syncronize records" option does nothing. I do sync all zones to all servers, and even though the zones on prod1 are the newest, they don't get pushed to all nameservers. Then i had the idea that if i alter the dns zones manually, then if i go in the interface and change the TTL, on prod1, then the prod1 zones should definitely be the newest in the cluster, however upon doing the ttl change, my NS3 and 4 records just got deleted! Why is that? Aren't the /var/named/$domain.db files the ones that are controling the thing? Any ideas would be appreciated.