The prerequisite bootstrapper (setup.exe) has a number of arguments that allow you to update it without having to regenerate the entire deployment package.
If you are planning on moving your ClickOnce package to a new server, this is important to note. If you're updating the -url, -componentsurl, or -homesite tags, you'll need to use the undocumented -dest flag.
-? : Show usage dialog.
-url or -componentsurl : Show the stored URL and components URL for this setup.
-url=<location> : Sets the URL source to the specified location.
-componentsurl=<location> : Sets the location to download prerequisites from. If it's blank, the prerequisites are downloaded from where the application is located or the homesite (if set).
-homesite=<true or false> : When set to true, downloads the components from their vendors' website, orverrides the components URL.
-dest=<name of new setup exe> : This is an undocumented flag. Use this when a new setup bootstrapper needs to be created with an updated URL, components URL, or homesite. You would do this by: 1) Copy setup.exe to foo.exe. 2) Run foo.exe to modify the original setup.exe: foo.exe /url=http://test/me /dest=setup.exe 3) Delete foo.exe.