btraill
My solution:
I overlooked the actual CTL website. It contains it's own explicit DNS records independent of the apex domain your panel is on. However, when I tried accessing these DNS records -- there was an endless spinning icon trying to load them. When I ran pdnsutil list-zone on the full A record of panel.apex.com it showed my outdated records on the DNS servers.
I used a similar approach as to what @rdbf did with the primary CTL addresses. Made an alias, set to primary, deleted previous primary and then restored. Something was wrong with the primary panel DNS fetching.
All is well now.
For anyone experiencing this and stopping:
boltflare
These errors are expected when run in certain contexts. You'll notice if you cd to that directory, the files are actually created.
The migration process is pretty seamless other than those minor hiccups.