mainViewport.Children.RemoveAt(i)

foreach (ScreenSpaceLines3D line3D in lines3DList)
            {
                lines3D.Points.Clear(); // Very importante
                _viewport3D.Children.Remove(lines3D);
             }

public ScreenSpaceLines3D()
{
    ...

    CompositionTarget.Rendering += OnRender; // <-- this line
}

public ScreenSpaceLines3D()
{
    ...

    // event registration removed
}

private bool AttachedToCompositionTargetRendering { get; set; }

protected override void OnVisualParentChanged(DependencyObject oldParent)
{
    base.OnVisualParentChanged(oldParent);

    var parent = VisualTreeHelper.GetParent(this);

    if (parent == null)
    {
        if (AttachedToCompositionTargetRendering)
        {
            CompositionTarget.Rendering -= OnRender;

            AttachedToCompositionTargetRendering = false;
        }
    }
    else
    {
        if (!AttachedToCompositionTargetRendering)
        {
            CompositionTarget.Rendering += OnRender;

            AttachedToCompositionTargetRendering = true;
        }
    }
}