iText-merged editable PDF loses form data when Acrobat Pro saves as separate PDF - pdf

Question

We're replacing Adobe LiveCycle Server with iText 5.4.1 in an existing webapp to merge XML data with LiveCycle Designer-generated PDF templates, generating editable PDF files from several hundred templates.
This code combines the data with the template, returning a PDF byte array:
// Import data into the PDF form
if (pdfTemplateFileName != null && inputXmlDataFile != null) {
// set up the objects
template = new PdfReader(pdfTemplateFileName);
filledPDF = new ByteArrayOutputStream();
stamper = new PdfStamper(template, filledPDF);
AcroFields form = stamper.getAcroFields();
// fill in the form with the data
XfaForm xfa = form.getXfa();
xfa.fillXfaForm(inputXmlDataFile);
//closing the stamper is necessary to flush to filledPDF
stamper.close();
returnPDF = filledPDF.toByteArray();
}
This code combines the PDF byte arrays into a portfolio:
List<byte[]> assemblingPdfList = assemblingPdfMap.get("newStyleForms");
// create PDF portfolio of editable documents
com.itextpdf.text.Document document = new com.itextpdf.text.Document();
ByteArrayOutputStream mergedPDFOutput = new ByteArrayOutputStream();
PdfWriter writer = PdfWriter.getInstance(document, mergedPDFOutput);
document.open();
Paragraph coverSheet = new Paragraph("Multiple files are bound together in this PDF Package");
coverSheet.setAlignment(com.itextpdf.text.Element.ALIGN_CENTER);
document.add(coverSheet);
// define the collection
PdfCollection collection = new PdfCollection(PdfCollection.DETAILS);
PdfCollectionSchema schema = new PdfCollectionSchema();
PdfCollectionField filename = new PdfCollectionField("Name", PdfCollectionField.FILENAME);
filename.setOrder(0);
schema.addField("FILENAME", filename);
PdfCollectionField description = new PdfCollectionField("Description", PdfCollectionField.TEXT);
description.setOrder(1);
schema.addField("DESCRIPTION", description);
PdfCollectionField modified = new PdfCollectionField("Modified", PdfCollectionField.MODDATE);
modified.setOrder(2);
schema.addField("MODIFIED", modified);
PdfCollectionField size = new PdfCollectionField("Size", PdfCollectionField.SIZE);
size.setOrder(3);
schema.addField("SIZE", size);
collection.setSchema(schema);
writer.setCollection(collection);
// loop through the PDF documents and add each to the portfolio
PdfFileSpecification fs;
PdfCollectionItem item;
int iNum = 0;
for (byte[] pdf : assemblingPdfList) {
fs = PdfFileSpecification.fileEmbedded(writer, null,
String.format("StylesResult_%s.pdf", iNum++), pdf);
fs.addDescription("Styles Result File", false);
item = new PdfCollectionItem(schema);
item.addItem("DESCRIPTION", "Styles Result File");
item.addItem("MODIFIED", new PdfDate() );
fs.addCollectionItem(item);
writer.addFileAttachment(fs);
}
// close document
document.close();
mergedPDFOutput.flush();
mergedPDFOutput.close();
return mergedPDFOutput.toByteArray();
At first, iText would not populate the form fields. We used LiveCycle Designer to change the data binding of most fields from Normal to Global, which enabled iText to populate most of them correctly. The exception were the repeating (think 'table') rows of data; setting the binding to 'Global' caused the first data value to be repeated down the column for each of the data records. Setting the repeating fields' bindings back to 'Normal' seemed to work.
The iText-merged editable PDF portfolios are launched in Internet Explorer 10. If we click 'Open File' to open an individual PDF in Adobe Acrobat XI Pro, all the data is there. However, if we click 'File' / 'Save As' in Acrobat Pro to save to a new PDF file, then open the new file, some or all of the form data has disappeared (In one case, the 'first generation' save left most of the data intact, but repeating subform data was erased. Saving again, creating a 'second generation' save, erased all data.)
My failed solution attempts include: (a) initializing PdfStamper in 'append' mode; (b) Modifying my PdfStamper with 'stamper.setEncryption(false, "", "", PdfWriter.ALLOW_{everything}...)'.
Adobe LiveCycle Server-generated portfolios do not lose data, no matter how many generations of saves are made.