(Requires gnu sed)
Moving to a new set of nameservers is a bit like moving house. Lots of stuff thrown away for reasons of unreasonable antiquity, lots of stuff could do with a refresh and cleanup.
sed -i.bak '/\(NS\|SOA\)/ s/\bdns1\.example\.org/innerdns1.example.org/g; /\(NS\|SOA\)/ s/\bdns2\.example\.org/innerdns2.example.org/g' master/*
This simple, pretty oneliner fixes NS and SOA records to point to new addresses, and leaves other records alone - unless you have really unfortunate and awkward capital-letter names in your zones. Add some more \b safeguards if so.