If the "Header & Navigation" settings are missing, it is likely your header is built using the theme builder. This theme builder header replaces the standard Divi header and in the process makes the header & navigation options in the customizer, which target the standard header, irrelevant. In recognition of this Divi hides the header & navigation options from the customizer, but the way in which it does so leaves the section briefly visible while the page loads. You may even manage to open the subsections (e.g. "Header Format", "Primary Menu Bar", "Secondary Menu Bar", "Fixed Navigation Settings" and "Header Elements"). Once the page is fully loaded the entire "Header & Navigation" section is hidden and the section below ("Footer") moves up to fill the gap.
In order to make changes to the header you need to instead go into the theme builder ("WP Dashboard > Divi > Theme Builder"), locate the relevant header layout and make the changes to it there.