Hello DigitalMage,
Thank you for providing as much information as you did. After seeing the name “Switch” I went out on a limb and it ended up being fruitful. The reason this isn’t being included is because of your folder named “Switch”. Along with PS4 and XboxOne, this is a special folder name according to the editor due to console packages. Anything in this folder will be excluded from packages that are not for that platform. I’m going to enter a bug report for it, but I don’t expect the functionality to be changed. The more likely solution is to add a warning or error message when either packaging or creating a folder with this name to warn about this.
In short; You’ll need to rename that folder and then everything should work fine.