John Hall wrote:
I'm in the process of migrating my installer from InstallShield to WiX 3. As part of this I have reorganised and rationalised the features in the product. When I come to do a major upgrade from the old installation to my new one, all of the features in my product in the customize dialog are unselected. If I install cleanly, they are all selected.

As always: Start with the verbose log. MSI will pass an ADDLOCAL property to the server when it comes to actually installing the product. I'm assuming you have RemoveExistingProducts scheduled early, so you can also check out InstallValidate action logging, to see the features and components that are getting removed (old version) and selected for install (new version).

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