I finally figured out what was going on. The stumbling block I had was how the non prime extensions were created. But also in my environment, they were completely a red herring.
For those struggling with how non prime extensions are created or how to manipulate them, this will help. Non prime extensions are created when you add an extension that doesn't already exist to a key on a phone. You can do this simply by going to Users and services configuration, selecting an existing phone, navigate to the keys tab, and add a key appearance for a new extension that doesn't yet exist. This extension that you put on the key is now a non prime extension. This extension can now be added to a hunt group or ring group and probably lots of other things.
To delete a non prime extension from the system, you will need to find each phone that has a key for the extension and delete all of those keys. You can find all the sets that have the key by navigating to Users and devices -> Advanced Configuration -> Multiline appearance Groups.
For those watching for what I was dealing with, the hunt group had a call rerouting rule that bounced calls to the external Esna voicemail system that had call routing voice menu tree for a mailbox associated with the hunt group. When users called the hunt group, the call rerouting routed the call to the voicemail which timed out immediately and sent the call to the number monitored on a key on the secretary's phone.
