Having an issue with WIX installer upgrade. Previously we had 2 version of installers 1 for per-machine and another for per-user.
Currently we have developed a dual mode
Per-user installs allow the installation of the same product multiple times for different users - and in different versions too. This makes upgrades and patches rather difficult to deal with, and I dislike this per-user concept altogether. I prefer to set the installer per-machine as standard. I don't feel that much is lost in functionality, but a lot is gained in managability. Though this is not an answer to your question, it is worth pointing out that per-user installs is a flawed concept - at best.
I don't know if it is an option to set your installer per-machine, but I found a way to migrate installs from per-user to per-machine automagically by using Installshield and its custom ISSetAllUsers custom action. The procedure is described here: windows Installer - uninstalling previous version when the versions differ in installation policy (per-user, per-machine)
Wix does not feature such a custom action as far as I know, but you could write your own custom action using the Win32 API call ::MsiEnumRelatedProducts()
as described by Rob Mensching here: how to change from per user to all user installation?
Here is a similar post for reference: How can a perUser installation program deal with a perMachine older version of the program?
Here is a blog describing (further) issues with per-user installs: Understanding “Per-User” or “Per-Machine” context for application Setup packages.
Let me add a couple of further comments: