有一个类似的问题。在我的例子中，我有一个视图控制器层次结构，其中一个子视图控制器有一个显示视图控制器。当我改变windows根视图控制器时，由于某种原因，显示视图控制器仍然在内存中。所以，解决方案是在我改变windows根视图控制器之前，先关闭所有视图控制器。

我在使用此代码时遇到此问题：

if var tc = self.transitionCoordinator() {

    var animation = tc.animateAlongsideTransitionInView((self.navigationController as VDLNavigationController).filtersVCContainerView, animation: { (context:UIViewControllerTransitionCoordinatorContext!) -> Void in
        var toVC = tc.viewControllerForKey(UITransitionContextToViewControllerKey) as BaseViewController
        (self.navigationController as VDLNavigationController).setFilterBarHiddenWithInteractivity(!toVC.filterable(), animated: true, interactive: true)
    }, completion: { (context:UIViewControllerTransitionCoordinatorContext!) -> Void in

    })
}

禁用这段代码，修复了这个问题。我设法让这个工作，只有启用这个过渡动画时，得到动画的过滤器条是初始化。
这并不是你真正要寻找的答案，但它可以为你找到正确的解决方案。

我最近遇到了一个类似的问题。我不得不手动从窗口中删除那个UITransitionView来修复这个问题，然后在以前的根视图控制器上调用dismiss来确保它的解除分配。
修复不是真的很好，但除非你找到了一个更好的方法，因为张贴的问题，这是唯一的事情，我发现工作！viewController只是newController从你原来的问题。

UIViewController *previousRootViewController = self.window.rootViewController;

self.window.rootViewController = viewController;

// Nasty hack to fix http://stackoverflow.com/questions/26763020/leaking-views-when-changing-rootviewcontroller-inside-transitionwithview
// The presenting view controllers view doesn't get removed from the window as its currently transistioning and presenting a view controller
for (UIView *subview in self.window.subviews) {
    if ([subview isKindOfClass:NSClassFromString(@"UITransitionView")]) {
        [subview removeFromSuperview];
    }
}
// Allow the view controller to be deallocated
[previousRootViewController dismissViewControllerAnimated:NO completion:^{
    // Remove the root view in case its still showing
    [previousRootViewController.view removeFromSuperview];
}];

雨燕3.0

(See其他Swift版本的编辑历史记录）
作为UIWindow上的一个扩展，允许传入一个可选的转换，这是一个更好的实现。

extension UIWindow {
    
    /// Fix for http://stackoverflow.com/a/27153956/849645
    func set(rootViewController newRootViewController: UIViewController, withTransition transition: CATransition? = nil) {
        
        let previousViewController = rootViewController
        
        if let transition = transition {
            // Add the transition
            layer.add(transition, forKey: kCATransition)
        }
        
        rootViewController = newRootViewController
        
        // Update status bar appearance using the new view controllers appearance - animate if needed
        if UIView.areAnimationsEnabled {
            UIView.animate(withDuration: CATransaction.animationDuration()) {
                newRootViewController.setNeedsStatusBarAppearanceUpdate()
            }
        } else {
            newRootViewController.setNeedsStatusBarAppearanceUpdate()
        }

        if #available(iOS 13.0, *) {
            // In iOS 13 we don't want to remove the transition view as it'll create a blank screen
        } else {
            // The presenting view controllers view doesn't get removed from the window as its currently transistioning and presenting a view controller
            if let transitionViewClass = NSClassFromString("UITransitionView") {
                for subview in subviews where subview.isKind(of: transitionViewClass) {
                    subview.removeFromSuperview()
                }
            }
        }
        if let previousViewController = previousViewController {
            // Allow the view controller to be deallocated
            previousViewController.dismiss(animated: false) {
                // Remove the root view in case its still showing
                previousViewController.view.removeFromSuperview()
            }
        }
    }
}

用法：

window.set(rootViewController: viewController)

或者

let transition = CATransition()
transition.type = kCATransitionFade
window.set(rootViewController: viewController, withTransition: transition)

这个问题困扰了我一整天，我尝试了@Rich的obj-c解决方案，结果发现当我想再显示一个视图控制器时，会被一个空的UITransitionView阻塞。
最后，我想出了这个办法，它对我很有效。

- (void)setRootViewController:(UIViewController *)rootViewController {
    // dismiss presented view controllers before switch rootViewController to avoid messed up view hierarchy, or even crash
    UIViewController *presentedViewController = [self findPresentedViewControllerStartingFrom:self.window.rootViewController];
    [self dismissPresentedViewController:presentedViewController completionBlock:^{
        [self.window setRootViewController:rootViewController];
    }];
}

- (void)dismissPresentedViewController:(UIViewController *)vc completionBlock:(void(^)())completionBlock {
    // if vc is presented by other view controller, dismiss it.
    if ([vc presentingViewController]) {
        __block UIViewController* nextVC = vc.presentingViewController;
        [vc dismissViewControllerAnimated:NO completion:^ {
            // if the view controller which is presenting vc is also presented by other view controller, dismiss it
            if ([nextVC presentingViewController]) {
                [self dismissPresentedViewController:nextVC completionBlock:completionBlock];
            } else {
                if (completionBlock != nil) {
                    completionBlock();
                }
            }
        }];
    } else {
        if (completionBlock != nil) {
            completionBlock();
        }
    }
}

+ (UIViewController *)findPresentedViewControllerStartingFrom:(UIViewController *)start {
    if ([start isKindOfClass:[UINavigationController class]]) {
        return [self findPresentedViewControllerStartingFrom:[(UINavigationController *)start topViewController]];
    }

    if ([start isKindOfClass:[UITabBarController class]]) {
        return [self findPresentedViewControllerStartingFrom:[(UITabBarController *)start selectedViewController]];
    }

    if (start.presentedViewController == nil || start.presentedViewController.isBeingDismissed) {
        return start;
    }

    return [self findPresentedViewControllerStartingFrom:start.presentedViewController];
}

好了，现在您要做的就是在切换根视图控制器时调用[self setRootViewController:newViewController];。

我尝试了一个简单的事情，为我工作的iOs 9.3：只需在dismissViewControllerAnimated完成期间从层次结构中删除旧viewController的视图。
让我们按照benzado的说明处理X、Y和Z视图：
也就是说，这一系列的操作...

1. X成为根视图控制器
2. X代表Y，因此Y的视图显示在屏幕上
   1.使用带有视图的过渡：使Z成为新的根视图控制器
   给予：

////
//Start point :

let X = UIViewController ()
let Y = UIViewController ()
let Z = UIViewController ()

window.rootViewController = X
X.presentViewController (Y, animated:true, completion: nil)

////
//Transition :

UIView.transitionWithView(window,
                          duration: 0.25,
                          options: UIViewAnimationOptions.TransitionFlipFromRight,
                          animations: { () -> Void in
                                X.dismissViewControllerAnimated(false, completion: {
                                        X.view.removeFromSuperview()
                                    })
                                window.rootViewController = Z
                           },
                           completion: nil)

在我的例子中，X和Y都很好地解除了分配，它们的视图不再处于层次结构中！