I am trying to sub-theme the Bootstrap theme. How do I remove the My account and Logout links from the navigation bar?
Try going to Appearance settings on your sub-theme
admin/appearance/settings/... and uncheck Secondary menu.
If that doesn't work, check menu settings at
admin/structure/menu/settings and make sure you haven't defaulted the main menu to "User menu".
Go to: admin/structure/block find user menu and set 'none', as region.
Simply, navigate to the user menu (admin/structure/menu/manage/user-menu) and deselect "enabled" for each item.