Updating ng-repeat scope removes unexpected items not in ng-repeat

Question

Why is my sortable angular ng-repeat menu deleting everything after the sorted menu item? https://github.com/RubaXa/Sortable/tree/dev I am using RubaXa's Sortable library with angular to make a sortable menu system for a custom CMS. When the menu gets sorted I have a this code loop through all menu items, record their location and update the $scope.menus.

            var menus = {};
            jQuery('.mb-draggable').has('a[href!="#"]').each(function(i, menuItem) {
                var location = jQuery(menuItem).parent('[data-menu]').data('menu');
                var position = jQuery('[data-menu="' + location + '"]').children('.mb-draggable').has('a[href!="#"]').index(jQuery(menuItem));  
                var id = jQuery(menuItem).data('id');

                //findMenuById finds the index and data of the menu item that has a matching id
                var found = theme.findMenuById($scope.menus, id);
                var newData = found.data;
                newData.location = location;
                newData.position = position;
                if(!menus[location]) {
                    menus[location] = [];
                }
                menus[location][position] = newData;
            });
            $scope.menus = menus;
            console.log('$scope.menus', $scope.menus);
            $scope.$apply();

$scope.menus has two different properties .main and .footer and each of these holds an array of menu list items. When I make $scope.menus = menus the $scope.menus is correct but the view suddenly gets rid of the footer menu and the editing buttons, which are not within ng-repeat. Here is the jade for the menu.

#navbar.navbar-collapse.collapse
        ul#sortable-head.nav.navbar-nav(data-menu="main")
            li(ng-repeat="menu in menus.main" class="mb-draggable {{menu.classes}}" ng-class="active(menu.url)" data-id="{{menu.id}}")
                a(href="{{menu.url ? menu.url : /}}" target="{{menu.target}}").mb-editable.mb-main-list-a {{menu.title}}
            li.drop-down
                a(data-toggle="dropdown" href="#").dropdown-toggle 
                    | Blog
                    span.caret
                ul#sortable-footer.dropdown-menu(role="menu" data-menu="footer")
                    li(ng-repeat="menu in menus.footer" data-id="{{menu.id}}").mb-draggable
                        a(href="{{menu.url ? menu.url: /}}" target="{{menu.target}}").mb-editable.mb-footer-list-a {{menu.title}}

The editing buttons are added on with jQuery

jQuery('[data-menu]').append($compile('<li data-toggle="modal" data-target="#editMenuItemModal" ng-click="selectedMenu($event)" class="mb-edit-menu-item"><a href="#"> <i class="fa fa-pencil fa-lg"></i></a></li>')($scope));

Answer 1

Use ng-sortable.js

Docs: https://github.com/RubaXa/Sortable/tree/dev#support-angularjs

P.S. If something is not clear, create an example on jsbin.com I will try to help you.