Reload AngularJS Controller
Solution 1:
Add this piece of code after the user is authenticated:
// To refresh the page
$timeout(function () {
    // 0 ms delay to reload the page.
    $route.reload();
}, 0);
Don't forget to include $timeout and $route in your controller. 
myapp.controller('HeaderController', ['$scope', '$location', '$window', 'AuthenticationService', '$timeout', '$route',
function HeaderController($scope, $location, $window, AuthenticationService, $timeout, $route)
Solution 2:
There's no need to reload your controller. Angular is smart enough to change the template when the $scope.isAuthenticated state changes.
One problem I see in your code is that once the $scope.isAuthenticated is defined it does not change anymore. I suppose you are setting AuthenticationService.isAuthenticated = true when user logs in but that change aren't being propagated to the $scope.isAuthenticated property because in JavaScript scalar values are copied by value instead of by reference.
There are many approaches, such as changing the AuthenticationService.isAuthenticated property from a boolean to a function:
angular.module('auth', [])
.factory('AuthenticationService', function () {
    // private state
    var isAuthenticated = false;
    // getter and setter
    var auth = function (state) {
        if (typeof state !== 'undefined') { isAuthenticated = state; }
        return isAuthenticated;
    };
    // expose getter-setter
    return { isAuthenticated: auth };
});
Then assign that function to the $scope:
$scope.isAuthenticated = AuthenticationService.isAuthenticated;
Then use the function in your template (don't forget the parens)
<app-header isauthenticated="{{ isAuthenticated() }}"></app-header>
Edit:
While writing a plunk to show you a working example I have realized that the link function of the directive is not called more than once, so as exposed in this stackoverflow thread I just modified the directive to observe changes in the isauthenticated attribute:
angular.module('directives', [])
.directive('appHeader', function() {
  var bool = {
    'true': true,
    'false': false
  };
  return {
    restrict: 'E',
    link: function (scope, element, attrs) {
      attrs.$observe('isauthenticated', function (newValue, oldValue) {
        if (bool[newValue]) { scope.headerUrl = 'authenticated.html'; }
        else { scope.headerUrl = 'not-authenticated.html'; }
      });
    },
    template: '<div ng-include="headerUrl"></div>'
  }
});
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