If I have say, an XML for my project which displays ads, I added the "AdMob" lines, save it, set the option "Do not overwrite the manifest file" and then compile my app, then I decide to use "Tools -> Clean Project", the "custom" XML is reset and I lose the AdMob additions, however the "android-Manifest-Example.xml" remains, if I set the XML to "read only" I get "access denied" when cleaning the project.
I think, the cleaning process should check for the "Do not overwrite manifest file" prior to start.