I’m on my phone so I can’t open your website preview. But I can guess some of the problems and possible fixes.
Problem one: make sure you’re styling the correct element. Navbars normally have a container inside it, so make sure you’re selecting the right Element when applying flexbox
Problem 2: you’re probably only affecting the opacity of the menu. To make the "mega menu " go away for real, you need to set its display to none. (Using some kind of drop-down is also a possible way for you to solve this problem)
Problem 3 : Make sure to place the mega menu inside the navbar, which I believe is set as sticky. If the mega menu is not placed as a child of the navbar , it’s not gonna move with it.
Tomorrow morning I’ll try to get a proper look at your website
Have a good night