The code below will create a webpart that can be added to any document library, when the button ‘Merge Reports’ is clicked it will merge all the documents together in the library in to a single document using Open XML SDK & Word Automation Services.

You will need to add the following references:

DocumentFormat.OpenXml
Microsoft.Office.Word.Server
Microsoft.Sharepoint
Microsoft.Sharepoint.Client
Microsoft.Sharepoint.Client.Runtime
Windows.Base

using System;
using System.ComponentModel;
using System.Web.UI;
using System.Web.UI.WebControls;
using System.Web.UI.WebControls.WebParts;
using Microsoft.SharePoint;
using System.Linq;
using System.IO;
using DocumentFormat.OpenXml.Packaging;
using DocumentFormat.OpenXml.Wordprocessing;
using System.Text;
using Microsoft.SharePoint.Client;
using ClientOM = Microsoft.SharePoint.Client;
using Word = Microsoft.Office.Word.Server;
using Microsoft.Office.Word.Server.Conversions;

namespace DocumentMerge.VisualWebPart1
{
    [ToolboxItemAttribute(false)]
    public class VisualWebPart1 : WebPart
    {
        // Visual Studio might automatically update this path when you change the Visual Web Part project item.
        private const string _ascxPath = @"~/_CONTROLTEMPLATES/DocumentMerge/VisualWebPart1/VisualWebPart1UserControl.ascx";

        protected override void CreateChildControls()
        {
            System.Web.UI.Control control = Page.LoadControl(_ascxPath);
            Controls.Add(control);
            base.CreateChildControls();
            Button btnSubmit = new Button();
            btnSubmit.Text = "Merge Reports";
            btnSubmit.Click += new EventHandler(OnSubmitClick);
            Controls.Add(btnSubmit);
        }

        void OnSubmitClick(object sender, EventArgs e)
        {
            // String to store the output path
            string outputPath = string.Format(@"{0}/masterreport-{1}.docx", SPContext.Current.RootFolderUrl, DateTime.Now.ToString("ddMMyyyy"));

            // String containing the blank document part for our new DOCX
            string strEmptyMainPart = "<?xml version='1.0' encoding='UTF-8' standalone='yes'?>" +
            "<w:document xmlns:w='http://schemas.openxmlformats.org/wordprocessingml/2006/main'>" +
            "<w:body><w:p><w:r><w:t></w:t></w:r></w:p></w:body></w:document>";

            // In-memory stream for our consolidated WSR DOCX.
            MemoryStream memOut = new MemoryStream();

            // Out output document's OpenXML object
            WordprocessingDocument outputDoc = WordprocessingDocument.Create(memOut, DocumentFormat.OpenXml.WordprocessingDocumentType.Document);

            MainDocumentPart mainPart = outputDoc.AddMainDocumentPart();

            Stream partStream = mainPart.GetStream();
            UTF8Encoding encoder = new UTF8Encoding();

            // Add our blank main part string to the newly created document
            Byte[] buffer = encoder.GetBytes(strEmptyMainPart);
            partStream.Write(buffer, 0, buffer.Length);

            // Save the document in memory
            mainPart.Document.Save();

            SPListItemCollection files = SPContext.Current.List.Items;

            int id = 1;
            foreach (SPListItem item in files)
            {
                SPFile inputFile = item.File;

                string altChunkId = "AltChunkId" + id;
                id++;
                byte[] byteArray = inputFile.OpenBinary();

                AlternativeFormatImportPart chunk = outputDoc.MainDocumentPart.AddAlternativeFormatImportPart(AlternativeFormatImportPartType.WordprocessingML,
                    altChunkId);

                using (MemoryStream mem = new MemoryStream())
                {
                    mem.Write(byteArray, 0, (int)byteArray.Length);
                    mem.Seek(0, SeekOrigin.Begin);
                    chunk.FeedData(mem);
                }

                AltChunk altChunk = new AltChunk();
                altChunk.Id = altChunkId;

                outputDoc.MainDocumentPart.Document.Body.InsertAfter(altChunk,
                    outputDoc.MainDocumentPart.Document.Body.Elements<Paragraph>().Last());
                outputDoc.MainDocumentPart.Document.Save();
            }

            outputDoc.Close();

            memOut.Seek(0, SeekOrigin.Begin);

            ClientContext clientContext = new ClientContext(SPContext.Current.Site.Url);
            ClientOM.File.SaveBinaryDirect(clientContext, outputPath, memOut, true);

            // Conversion

            string docPath = string.Format(@"{0}{1}", SPContext.Current.Site.Url.Replace(@"\\", ""), outputPath);
            //string pdfPath = docPath.Replace(".docx", ".pdf");

            ConversionJobSettings JobSettings = new ConversionJobSettings();
            JobSettings.OutputFormat = SaveFormat.Document;
            JobSettings.OutputSaveBehavior = SaveBehavior.AlwaysOverwrite;

            ConversionJob ConvJob = new ConversionJob("Word Automation Services", JobSettings);
            ConvJob.UserToken = SPContext.Current.Site.UserToken;
            ConvJob.AddFile(docPath, docPath);
            ConvJob.Start();

        }
    }
}

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