We use wix to create setups for our application. For the case where the user has already installed an older version of our application, we do a major upgrade with the MajorU
I implemented Mike Fuchs approach, and while it did technically work (aka install functioned as expected), the program did not appear in APR for other users.
In thinking this over, it makes sense because how would the installer know that all per-user installs were removed/updated to the new perMachine version.