When you adapt a project to Android, there are two type of files that are generated. There's the files you have to be able to edit, like AndroidManifest.xml. And there's the files that you should not edit, which have to be updated every time the source files in Qt are updated and when you make some changes to your project. These are the .java files in Origo for instance.
These need to be separated logically. The files you are not supposed to edit need to actually update when the source files update, and they should be deleted when you clean the project etc.