You can have a lot of errors like below inside your logs which indicate a broken named.conf file
Apr 14 08:32:17 server1 pdns_server: Backend reported condition which prevented lookup (Zone for ‘sub.domain.com’ in ‘/var/named/sub.domain.com.db’ temporarily not available (file missing, or master dead)) sending out servfail
Backup your current named.conf file
mv -v /etc/named.conf /etc/named.conf_old
Run the following to rebuild the proper /etc/named.conf file
/usr/local/cpanel/scripts/rebuilddnsconfig
Restart your pdns server
/scripts/restartsrv_pdns
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