I found out the hard way that this is not pretty. In the long run, you'll have to have all users completely uninstall and reinstall their apps. Here are more details...
[A New DevLife post]
Changing the target processor type of deployed ClickOnce applications
Wednesday, February 18 2009 - dotNET
- #1 Hector Correa on 2.18.2009 at 5:52 PM
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To make matters worst, the shortcut that ClickOnce applications get when they are first installed ALSO list this parameter (e.g. "processorArchitecture=msil") at the end of the command line that fires your application. So even if you get everything in synch (your project and your Manifest) users that already have the app installedhave it "hard coded" already in their shortcut.(BTW, comments do not seem to work in the DevLife site, I got "Invalid request" from Movable Type when I tried to comment there)
