@chuck_b Yes, whenever you update all installed packages or just ES from the setup script.
I would keep a copy of the new ES binary with the remapped quit key and then, after updating, you can overwrite the ES binary with your modded version, unless, of course, there is a new feature in ES that you desire, in which case, you would need to recompile.
Slight correction to my above post. After restarting the pi, the stop emulationstation and start emulationstation script no longer works. It is stopping emulationstation but no longer will resume it.
I think you will want to setup another command in emulators.cfg where you could give your version a name and use Runcommand to select it for ROMs as needed.
This looks like it can do exactly what I need. Thank you!