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From WiX Wiki at MindCapers

> When I install then uninstall my app all registry keys created on 
> install are completely removed as expected. However if I apply a patch 
> to the install and then attempt to uninstall the original application, 
> the registry keys are left behind -- but everything else is removed.
> Could someone help me out with why I am seeing this behaviour?
>

First step is always a verbose log. Check around the InstallValidate 
action to see what actions MSI is planning on taking with each 
component, patched and unpatched.

> I finally worked out why I was having issues uninstalling my patch and 
> thought I would share the solution in case others come across it. The 
> problem was the version of MsiMsp.exe and PatchWiz.dll that I was 
> using to create the patch -- I was using Windows Installer 3.0 to 
> install the patch but not the correct components to create it. I 
> upgraded to the latest version and it all works like a dream.
>

MSI is highly backward compatible but later versions of the SDK tools 
support later versions' features. It's always explicit, however, so you 
can target prior versions of MSI. And, of course, later versions have 
bug fixes, so it's generally preferable to use the latest release.