I seriously doubt that happened here, either. I'm unfamiliar with the Church's franchise agreement, but I'm absolutely positive it didn't contain any language about the menu. Typically, that sort of stuff is included in the manual, which is separate and apart from the franchise agreement. The franchise agreement will ALWAYS allow the franchisor, in its sole discretion, to change the manual at any time.
Just as an aside, Chick-fil-a disclaims franchise status. I think it is a franchise, but it claims that it's not. For whatever it's worth.
You're unfamiliar with it, yet you're certain about what it contains?
Who are you? God?