If I am understanding correctly, you’re just wanting to ensure that the only pages displayed in the dropdowns at the top of the page. Unlike many other WYSIWYG editor out there, the pages that are listed in your “Pages” menu don’t automatically reflect in your navigation-bar of the site. While the may seem like an annoyance, it actually gives you more versatility on customization.
With this in mind, in order to add your new pages to the dropdown menus, you will simply need to open up each dropdown within the nav-menu, then delete each of the unused links. I suggest leaving one link in each dropdown. This will allow you to customize the text and link within and keep the formatting without having to built a new element yourself.
Here is a picture of where you can find the dropdown menus and the links within the navigation:
Let me know if I need to further clarify anything!