Hello Brad Thompson
There is a way. You have to take a separate file (for example: mymenu.php)
templates/shaper_helixultimate/features/mymenu.php
There is a class HelixUltimateFeatureMenu in menu.php file. In your file, you have to change it to HelixUltimateFeatureMymenu.
Then you have to do the same on the Header. For example, you will use style 1 header. So, you have to take a new file (for example: myheader.php)
templates/shaper_helixultimate/headers/style-1/myheader.php
There you have to update the path as include_once $feature_folder_path . '/mymenu.php'; and update HelixUltimateFeatureMymenu
Then if you install the template again, it will update original menu.php and header.php. Your mymenu.php and myheader.php will be safe.
Best regards