Sorry, when you said “if so we are not using it”, I thought you are referring to ‘Admin Menu Editor’ functionality not the plugin.
Now that I understand that you are not using(deactivated) the plugin, it cannot alter/change your menu configuration. Menus work in WordPress based on the capabilities the logged in user has. You just need to make sure that, the logged in user has all the capabilities the menu is looking for. It doesn’t matter whether it comes from a single role or multiple roles.
For example ‘Posts’ uses ‘edit_posts’ capability.