Changing root view controller after iOS app has loaded.

it should still fix some issue I want to change the Text color and the background color of the left hand side of the RootView Controller in my UISplitView controller. This needs to happen in both orientations. , To change the text color:

// Dequeue or create a cell of the appropriate type.
UITableViewCell *cell = [tableView dequeueReusableCellWithIdentifier:CellIdentifier];
if (cell == nil) {
    cell = [[[UITableViewCell alloc] initWithStyle:UITableViewCellStyleDefault reuseIdentifier:CellIdentifier] autorelease];
    cell.accessoryType = UITableViewCellAccessoryNone;
}

// Configure the cell.
cell.textLabel.text = [[data objectAtIndex:indexPath.row] retain];
cell.textColor = [UIColor blueColor]; //Here you can use whatever color you want
return cell;

I think the issue was by ths following , This was actually pretty simple, and has nothing to do with segues.
I was expecting a rootViewController property on UINavigationController objects while overlooking the @property UIViewController* topViewController.

// Load the map's navigation controller from storyboard
MyMapNavigationController* mapNavigation = [self.storyboard instantiateViewControllerWithIdentifier:mapNavigtionIdentifier];

// ECSlidingViewController API to set hidden view controllers
self.slidingViewController.underRightViewController = mapNavigation;

// Grab root view controller
MyMapController* map = mapNavigation.topViewController;

// Slightly hacky magic
[map view]; //lazily instantiated property will initialize view and controller when called. 

seems to work fine You could assign the UINavigationController a delegate and implement the method -

- (void)navigationController:(UINavigationController *)navigationController
      willShowViewController:(UIViewController *)viewController
                    animated:(BOOL)animated {
     // check viewController is kind of class, check any flags

     // pass object to vc

}

Hope that helps It is not recommended behavior to change the view of a UIViewController past the point in time at which loadView is called. You'll want your view controller to have one, persistent view for its lifetime. I'd recommend one of the following.
Layering the table view / collection view on top of your view controller's view. That way you're not monkeying with the main underlying view itself. Having two instances of your view controller, one with a table and the other with a collection view, and swapping between those.