The old version of the setup was created with InstallScope=\"PerMachine\". The new version is intended to have InstallScope=\"PerUser\"; it also needs to u
You should define what kind of upgrade you are doing, and if it's a major upgrade then where is it sequenced in your major upgrade element, although...
Probably the main issue is that cross context major upgrades aren't supported by Windows Installer, so if you are doing a major upgrade you will end up with both products installed. That's not an upgrade, that's most likely just a collision. So assuming that you want only one of them to be installed at the end of all this, you will need to uninstall the older per-machine installation and then install the per-user. As to why the uninstall of the per-machine product doesn't remove the registry keys, there are many possible reasons, such as they were created by the app not the MSI, or the component was marked permanent, or the component has another client product on the system - a log of the uninstall might show what's going on.
I have to add this as an answer, too long as a comment. I will "evolve" it once you provide more information:
Why do you want to switch to per-user installation? In the MSI world this is not an ideal way to deploy. An application is usable per-user even if installed per machine. With a per-machine install you simply add the ability to write shared settings that should not be overridden by a user. And your application is easier to upgrade, uninstall, patch and manage overall.
Here are a few more links to explain some of the problems with per-user setups. They are real, I am only trying to warn people what problems they are most likely going to face (almost certainly going to face):
Are you deploying HKCU or HKLM keys? I would not recommend writing any HKCU values from your setup, they should be written by the application itself. A setup is for writing to HKLM and other places that require "elevated rights". It should never be used to write user preferences. There will be interference when you do upgrades (as you have experienced).
I am sure that we can make all these problems go away if you follow our advice precisely. You are facing a very common MSI problem.
Let me attempt a tentative answer without having all the information:
HKCU\Software\MyCompany\MyApp\5
instead of HKCU\Software\MyCompany\MyApp
. This "decouples" your old and new state, and you got room to maneuver and clean up things.HKLM\Software\MyCompany\MyApp\5\MyAppHKLMKeyPath = 1