ParentTree Objects do not match KArray objects after merge

public void testStructureTreeMerge3() throws IOException
{
    PDFMergerUtility pdfMergerUtility = new PDFMergerUtility();
    PDDocument src = PDDocument.load(new File(SRCDIR, "reading-order.pdf"));
    PDDocument dst = PDDocument.load(new File(SRCDIR, "reading-order.pdf"));
    pdfMergerUtility.appendDocument(dst, src);
    src.close();
    dst.save(new File(TARGETTESTDIR, "reading-order-merged.pdf"));
    dst.close();

    PDDocument doc = PDDocument.load(new File(TARGETTESTDIR, "reading-order-merged.pdf"));
    assertTrue(checkAnnotationMatches(doc.getDocumentCatalog().getStructureTreeRoot().getKArray(), doc.getDocumentCatalog().getAcroForm().getFields(), (COSArray)doc.getDocumentCatalog().getStructureTreeRoot().getParentTree().getCOSObject().getDictionaryObject(COSName.NUMS)));
}
private boolean checkAnnotationMatches(COSArray kArray, List<PDField> acroformFields, COSArray numbersArray) {
    for (int i = 0; i < kArray.size(); i++) {
        COSBase entry = kArray.get(i);
        if (entry instanceof COSArray){
            COSArray entryAsArray = (COSArray) entry;
            if (!checkAnnotationMatches(entryAsArray, acroformFields, numbersArray)) {
                return false;
            }
        } else if (entry instanceof COSInteger) {
            //do nothing, just need to screen these out so next line doesn't blow up
        } else if (((COSObject) entry).getObject() instanceof COSDictionary){
            COSDictionary entryDictionary = (COSDictionary)((COSObject) entry).getObject();
            if (entryDictionary.getItem(COSName.K) != null) {
                COSBase kids = entryDictionary.getItem(COSName.K);
                if (kids != null) {
                    if (kids instanceof COSInteger) {
                        //do nothing, don't care about marked content tags
                    } else if (kids instanceof COSDictionary) {
                        COSDictionary kidsAsDictionary = (COSDictionary) kids;
                        if (!checkForMatches(kidsAsDictionary.getDictionaryObject(COSName.OBJ), acroformFields, numbersArray)) {
                            return false;
                        }
                    } else if (kids instanceof COSArray) {
                        COSArray kidsAsArray = (COSArray) kids;
                        if (!checkAnnotationMatches(kidsAsArray, acroformFields, numbersArray)) {
                            return false;
                        }
                    }
                }
            } else if (entryDictionary.getDictionaryObject(COSName.OBJ) != null) {
                if (!checkForMatches(entryDictionary.getDictionaryObject(COSName.OBJ), acroformFields, numbersArray)) {
                    return false;
                }
            }
        }
    }
    return true;
}
private boolean checkForMatches(COSBase objectReference, List<PDField> acroformFields, COSArray numbersArray) {
    boolean result = false;
    for (PDField field : acroformFields) {
        if (field.getCOSObject() == objectReference && numbersArray.indexOfObject(objectReference.getCOSObject()) > 0) {
            result = true;
        }
    }
    return result;
}