using System;

using System.Xml;

using System.Xml.Linq;

using System.Linq;

using System.Xml.XPath;

using System.Collections.Generic;

public class Program

{

    public static void Main()

    {

        var raw1 = @"<System>

    <Configurations>

​

        <Configuration>

            <Domain>MyDom01</Domain>

            <Components>

                <Component>

                    <Name>Memory</Name>

                    <Size>16</Size>

                </Component>

                <Component>

                    <Name>CPU</Name>

                    <Size>8</Size>

                </Component>

            </Components>

        </Configuration>

​

        <Configuration>

            <Domain>MyDom02</Domain>

            <Components>

                <Component>

                    <Name>CPU</Name>

                    <Size>12</Size>

                </Component>

            </Components>

        </Configuration>

​

    </Configurations>

</System>";

        var raw2 = @"<System>

    <Configurations>

​

        <Configuration>

            <Domain>MyDom01</Domain>

            <Components>

                <Component>

                    <Name>Memory</Name>

                    <Size>128</Size>

                </Component>

                <Component>

                    <Name>CPU</Name>

                    <Size>32</Size>

                </Component>

                <Component>

                    <Name>CPU</Name>

                    <Size>32</Size>

                </Component>

            </Components>

        </Configuration>

​

        <Configuration>

            <Domain>MyDom02</Domain>

            <Components>

                <Component>

                    <Name>Memory</Name>

                    <Size>32</Size>

                </Component>

            </Components>

        </Configuration>

​

        <Configuration>

            <Domain>MyDom03</Domain>

            <Components>

                <Component>

                    <Name>Memory</Name>

                    <Size>32</Size>

                </Component>

            </Components>

        </Configuration>

​

    </Configurations>

</System>

";

        var xdoc1 = XDocument.Parse(raw1);

        var xdoc2 = XDocument.Parse(raw2);

​

        foreach (var item in xdoc2.Descendants("Configuration"))

        {

            var domain = (string)item.Element("Domain");

            var parent = xdoc1.Descendants("Configuration")

                .Where(o => (string)o.Element("Domain") == domain)

                .Elements("Components")

                .FirstOrDefault();

            if(parent != null) 

            {

                parent.Add(item.Elements("Components").Elements("Component"));

            } 

            else 

            {

                xdoc1.Root.Element("Configurations").Add(item);

            }

        }

​

        System.Console.WriteLine(xdoc1.ToString());

    }

}