Code

var containerRect = ...;
diagram.RealizeItems(containerRect);

var copyItems = new DiagramItemCollection();
foreach (var item in diagram.Items)
	if (containerRect.IntersectsWith(item.GetBounds()))
		copyItems.Add(item);

var tempDiagram = new Diagram();
tempDiagram.PasteSelection(
	diagram.CopySelection(copyItems, false, true),
	null, new Vector(0, 0));

foreach (var item in tempDiagram.Items)
{
	var container = item as ContainerNode;
	if (container != null &&
		containerRect.IntersectsWith(item.GetBounds()))
	{
		container.Arrange(...);
	}
} 

Code

public virtual bool Arrange(VirtualizingDiagram diagram, IEnumerable<object> items);
public virtual bool Arrange(VirtualizingDiagram diagram);
public virtual bool Arrange(Diagram diagram, DiagramItemCollection items);
public virtual bool Arrange(Diagram diagram); 

Code

container.Arrange(layout);
container.UpdateBounds(true); // make space for the right link too

...

for (int i = 0; i < copyItems.Count; i++)
{
	var link = copyItems[i] as DiagramLink;
	if (link != null)
	{
		var tempLink = (DiagramLink)tempDiagram.Items[i];
		var linkData = (LinkData)link.DataContext;
		linkData.ControlPoints = tempLink.ControlPoints;
		link.ControlPoints.Clear();
		link.ControlPoints.AddRange(tempLink.ControlPoints);
		link.UpdateFromPoints();
	}
	var node = copyItems[i] as DiagramNode;
	if (node != null)
	{
		var tempNode = (DiagramNode)tempDiagram.Items[i];
		var nodeData = (NodeData)node.DataContext;
		nodeData.Width = tempNode.Bounds.Width;
		nodeData.Height = tempNode.Bounds.Height;
		nodeData.X = tempNode.Bounds.X;
		nodeData.Y = tempNode.Bounds.Y;
		node.SetBounds(tempNode.Bounds, false, false);
	}
}

public class NodeData : INotifyPropertyChanged
{
...
	private double width;
	public double Width
	{
		get { return width; }
		set
		{
			if (width != value)
			{
				width = value;
				PropertyChanged?.Invoke(this, new PropertyChangedEventArgs("Width"));
			}
		}
	}

	private double height;
	public double Height
	{
		get { return height; }
		set
		{
			if (height != value)
			{
				height = value;
				PropertyChanged?.Invoke(this, new PropertyChangedEventArgs("Height"));
			}
		}
	}
...