I had exactly the same, resulting in a black screen without resetting back. For me the combination of the following code did the trick. First, reset the secondWindow, second, reassign your main screen to make it work with touches again.
// Reset the second window
self.secondWindow.frame = CGRectZero;
self.secondWindow.screen = nil;
self.secondWindow = nil;
// Reassign your main screen to make it work with touches again
UIWindow *mainScreen = [[[UIApplication sharedApplication] windows] firstObject];
[mainScreen makeKeyAndVisible];