Hi there,
we don’t recommend importing a site on a pre-built site, if you do its always best to make a backup before doing so.
Importing the Theme will not remove any content you already have, it will just swap out things such as Menus. So the Header Element will still exist, it may require you to re-assign it to a page depending on the display rules you set.
You can also export Header Elements, as they are a Post Type using the Dashboard > Tools > Export ( and import )