The scenario where pre-requisites change during the lifecycle of an application is not explicitly supported. However, with ClickOnce, if a customer re-runs the Bootstrapper, then any missing pre-requisites will be installed and then the application launched after it's run, so it can be done. The trick, however, is to alert your users who have already installed your app that they need to re-run the bootstrapper. There are a couple ways I can think of to do that.
1) Release an update to your Ver-1 application that uses the System.Deployment API's to determine if there's an update. If there is, it displays some UI to tell (or provide a link) the user to go to the web page, and then run the bootstrapper. Then, you wait until that has propagated, and then release your next update. As you can see, there are probably some issues with this approach.
2) Figure out where your application will break, i.e. throw an exception, if the prerequisites aren't there. In your new version of the app, catch those exceptions and then show UI that directs the user to re-running the bootstrapper to fixup the problem. I'm really starting to think that applications that can detect these kinds of installation problems are a good practice because they will also detect, and direct to repairing, problems that can occur after the application has been succesfully installed and used, like if someone goes to the AddRemove programs utility and removes something they didn't realise your app depended on.
Hope this helps...