The only way to update the prerequisite is for the user to run setup.exe again. For something major, like changing the .Net Framework, you pretty much have to uninstall and reinstall the application. You can do this programmatically, which is explained in this article:
http://robindotnet.wordpress.com/2009/03/30/clickonce-and-expiring-certificates/Another idea is to have your ClickOnce application keep track of what version the user is currently using, as well as what version you WANT the user to use. You could store the one you WANT the user to use in the application settings, and the one the user is using in the user settings, and compare them to see if a new version is available. When a new version is available, pop up a window asking him if it's okay for you to download and install it, and if he says yes, download it in the background and then run it.
It just depends on your configuration, your setup, what your application does, etc.
RobinDotNet
Click here to visit my ClickOnce blog!