Hi,
I looked at this in some more detail - it looks like it's actually quite complex to do a full MSI update to the registry - from what I can see, it requires knowing the installed application's Update Code GUID, and then updating the Product Code GUID as well as the version.
If you have a solution or any suggestions, that would be great. In the meantime, I've come up with a solution: instead of specifying the files of my application inside wyBuild, I simply added the installer for the new version, and flagged it it as "Execute after update". Thus it just downloads and runs my regular installer.
I realize this goes against some of the core value of wyBuild - namely, making a small download of just the deltas from the previous version - but it still allows use of a lot of your automation features and is still a heck of a lot better than having to code it all myself.