Hi CodeCrew,
How can I disable the alert showing up when changing the alternate app icon? Is there any method to disable it?
There is no supported way of doing so; although there might be private APIs that let you do it, you run the risk of Apple rejecting your app.
According to the appropriate section of the Human Interface Guidelines: “Note that your app icon can only be changed at the user’s request and the system always provides the user with confirmation of such a change.”