Unir dois arquivos PDF em um

...
byte [] pdfBytes1 = Base64Utils.fromBase64String(String pdf1Base64); // Vc pode criar esse utilitário para converter o texto de base64 para binário
byte [] pdfBytes2 = Base64Utils.fromBase64String(String pdf2Base64);

// Se nao me engano os métodos da API do IText podem aceitam byte[] também,
// mas caso não leia faça assim
InputStream pdfStream1 = new ByteArrayInputStream(pdfBytes1);
InputStream pdfStream2 = new ByteArrayInputStream(pdfBytes2);
InputStream [] array = new InputStream[]{pdfStream1, pdfStream2};
// Agora vc faz o merge
...

import com.itextpdf.text.Document;
import com.itextpdf.text.pdf.BaseFont;
import com.itextpdf.text.pdf.PdfContentByte;
import com.itextpdf.text.pdf.PdfImportedPage;
import com.itextpdf.text.pdf.PdfReader;
import com.itextpdf.text.pdf.PdfWriter;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

public class MergePDF {
 
    public static void main(String[] args) {
        try {
            List<InputStream> pdfs = new ArrayList<InputStream>();
            pdfs.add(new FileInputStream("C:/Users/Eduardo/Desktop/TESTE_MERGE/1.pdf"));
            pdfs.add(new FileInputStream("C:/Users/Eduardo/Desktop/TESTE_MERGE/2.pdf"));
            pdfs.add(new FileInputStream("C:/Users/Eduardo/Desktop/TESTE_MERGE/3.pdf"));
            pdfs.add(new FileInputStream("C:/Users/Eduardo/Desktop/TESTE_MERGE/4.pdf"));
            OutputStream output = new FileOutputStream("C:/Users/Eduardo/Desktop/TESTE_MERGE/saida.pdf");
            MergePDF.concatPDFs(pdfs, output, true);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
 
    public static void concatPDFs(List<InputStream> streamOfPDFFiles,
            OutputStream outputStream, boolean paginate) {
 
        Document document = new Document();
        try {
            List<InputStream> pdfs = streamOfPDFFiles;
            List<PdfReader> readers = new ArrayList<PdfReader>();
            int totalPages = 0;
            Iterator<InputStream> iteratorPDFs = pdfs.iterator();
 
            // Create Readers for the pdfs.
            while (iteratorPDFs.hasNext()) {
                InputStream pdf = iteratorPDFs.next();
                PdfReader pdfReader = new PdfReader(pdf);
                readers.add(pdfReader);
                totalPages += pdfReader.getNumberOfPages();
            }
            // Create a writer for the outputstream
            PdfWriter writer = PdfWriter.getInstance(document, outputStream);
 
            document.open();
            BaseFont bf = BaseFont.createFont(BaseFont.HELVETICA,
                    BaseFont.CP1252, BaseFont.NOT_EMBEDDED);
            PdfContentByte cb = writer.getDirectContent(); // Holds the PDF
            // data
 
            PdfImportedPage page;
            int currentPageNumber = 0;
            int pageOfCurrentReaderPDF = 0;
            Iterator<PdfReader> iteratorPDFReader = readers.iterator();
 
            // Loop through the PDF files and add to the output.
            while (iteratorPDFReader.hasNext()) {
                PdfReader pdfReader = iteratorPDFReader.next();
 
                // Create a new page in the target for each source page.
                while (pageOfCurrentReaderPDF < pdfReader.getNumberOfPages()) {
                    document.newPage();
                    pageOfCurrentReaderPDF++;
                    currentPageNumber++;
                    page = writer.getImportedPage(pdfReader,
                            pageOfCurrentReaderPDF);
                    cb.addTemplate(page, 0, 0);
 
                    // Code for pagination.
                    if (paginate) {
                        cb.beginText();
                        cb.setFontAndSize(bf, 9);
                        cb.showTextAligned(PdfContentByte.ALIGN_CENTER, ""
                                + currentPageNumber + " of " + totalPages, 520,
                                5, 0);
                        cb.endText();
                    }
                }
                pageOfCurrentReaderPDF = 0;
            }
            outputStream.flush();
            document.close();
            outputStream.close();
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            if (document.isOpen())
                document.close();
            try {
                if (outputStream != null)
                    outputStream.close();
            } catch (IOException ioe) {
                ioe.printStackTrace();
            }
        }
    }
}