Unfortunately, the behavior you speak of is intended.  Do you have changes to the header that often?  What kind of changes?  There may be a way to workaround your frequent changes without having to repackage the skin everytime.

That's what I was thinking.  That is why I wanted to know what kind of changes he makes.  Then we could determine if there is a way to accoplish this using a pane/container/module approach.  Or, perhaps a Skin Object.