Mass Selector in DNS Zone Manager
Supposing you have a customer with 29 subs.
With added service subdomains enabled, you are looking at something close to 21 x 29 = 609 DNS records.
In a situation where these didn't appear in the Domains >> Subdomains after migration, you need to re-add these records.
It means either deleting these manually (before adding them to a cluster) or writing a script for that.
Something like the "servicedomains" script to remove customer-added subdomains will be great.
But equally important is having a function in DNS Functions >> DNS Zone Manager >> $domain to mass select/delete these as you would do with Transfer.