Unable to Edit Main Navigation Drupal 8
It's kinda hard to test for the ones not having this theme.

Looking at the demo for the theme I can see it is using Superfish module to display this menu.

So, after removing the menu element try to flush the cache (from /admin/config/development/performance). If still doesn't work, go check on Structure->Blocks and see the superfish block... click on configure and be sure it is using the same menu. You have more settings in there, and you can look into the module (Superfish) settings, too.