Hey Dave,
We have a number of customers using WiX with wyUpdate successfully.
If I install 1.0 with a WiX installation, then update to 1.1 with wyUpdate will uninstall via Programs and Features uninstall all extra resources, files added via the 1.1 wyUpdate?
Use wyUpdate's /uninstall commandline option from within your WiX uninstaller.
Will a matching 1.1 WiX installer be able to cleanly repair and/or uninstall a 1.1 installation updated via wyUpdate as above?
If a users "repairs" the installation then they'll go back to the "1.0" version of your app, unless you also update the necessary WiX files (in which case a "repair" will go the the latest clean version). Or execute a dummy WiX installation that makes the necessary changes.
Basically I want users to be able to get to 1.1 either by a standard WiX 1.1 installer (running fresh, or a major upgrade over 1.0) or via wyUpdate without running into installation integrity issues if they mix and match.
So long as you disable "advertised shortcuts" (see step 5 of the step-by-step walkthrough) then everything will work fine.
Does that make sense?