I recently had a certificate expire in a WinForms application that I deploy with ClickOnce. I created a new test certificate and released an update. All users that had Windows 7 got an error that told them the application failed to run. Other users who run Windows XP had no issues.
The program is using the .NET 4.0 Framework. I am programming it in Visual Studio 2010.
That article led me to believe that there shouldn't be any issues with attaching a new certificate to the program.