Why won't my custom content field update on save/edit?
I figured out what my issue was. In order to force users to use the UI I set the input field as being disabled from my JS file.

 document.getElementById('edit-brand-header-config-und-0-value').disabled = true; 


Apparently setting it to disabled prevents it from being stored even though I could add a value to it programmatically through JS.

Removing "disabled = true"