Hi Chris,
If you don't mind hacking the code, you can find the codes that build the flatnav in lib/navigationlib.php
Look for
class flat_navigation extends navigation_node_collection
In the intialise function, all the codes that build the flatnav happen
This link is also useful
https://docs.moodle.org/dev/Boost_Navigation
Apparently, from what I understood, when Moodle build the navigation link, it flags those navigation links which are suppose to appear in the flat navigation. In the intialise function it basically loop through all the navigation links and add to the flat navigation if the value of
$coursenode->showinflatnavigation = true;