Ouch, that’s a tough one. You might be able to add some custom code to the lightbox and maybe change the z-index. Maybe? I’ve customized lightbox elements before by making a hidden page with divs using the same names. They all start with “w-lightbox-xxxxx”.
have you looked at the published site in the Chrome inspector to see what the z-index of the nav is at runtime? Could you share a link to the published site?