I just sent you a Private Message (since I will need sensitive information) requesting more information. Please respond to that whenever you get a chance. Thanks!
This new functionality of msi 3.0 (ability to uninstall individual patches) will cause the problem you mention. This is because the merge module doesn't run a re-register custom action during the patch uninstall. We're talking to the Windows Installe...
This is not a supported API so it's intentionally left out of the documentation. It's been around since version 2 or 3. I'm not quite sure what it's supposed to do either. The "Download" and "Execute" APIs are the ones most commonly used to have more...
This has been corrected. Additionally I have attached the 4.1 help file so that you don't have to re-download the entire SDK. Thanks for pointing this out!