By header, do you mean the logo image?
If you access and then update a portal's site settings by reaching ithe page via the Host, Portals menu of another portal, you will lose the target portal's logo setting. I think this was fixed in 4.8.something, but it was certainly going on in a few previous versions. Perhaps that is what has happened.
The solution is to upgrade and/or only apply site settings when directly signed into the target portal.
Rob