I have tested the delete of all .h header files before any build (win7 desktop Netbeans and command prompt) with the exception of leaving these that do not update:
They are generated new in the src/native/cpp folder and copied into the build/lib SnapShot-sources jar with new timestamps. If after that first build/copy you just leave the header files alone in the src/native/cpp folder, they are not copied. The timestamp doesn’t change in build/lib SnapShot-sources jar.
What would be a solid way to test this in game?