Is there a function that is able to recognize existing headers and footers and “flatten” them so that they cannot be changed using a pdf editor?

Question

I am merging multiple pdf files using Java and Apache PDFBox; each file has multiple pages. Each page has footer and header on it (page number, reference number). When I flatten the files and merge the files, the page numbers remain dynamic. That is to say, when I go into my pdf editor program and add a secondary page number the original page numbers change as well. For example, I have two files with three pages in them. The page numbers are centered and read “Page 1 of 3”, etc. When I flatten them and then combine them, I would like to add a secondary page number on the left footer that will read “Page 1 of 6” without altering the center bottom page number which should still read as “Page 1 of 3”. I am of the impression that page footers and headers are not considered page labels or annotations.

It is my understanding that within pdf files Page headers and footers are usually placed automatically as a function of pagination. As such this content is not part of the reading-order of the document and is not considered to be “real content”, per PDF Association "Tagged PDF Best Practice Guide: Syntax", section 3.71.

I am using NetBeans IDE with Maven and Apache's pdfbox.

How do I extract the "header/footer" from my existing PDF file and write the information, as content, to a new file with the same fonts and in the same location as the original files

Image of pdf file is below.

Here is a snippet from one of my simpler attempts to flatten a file. For some odd reason the pre-existing headers and footers are not affected.

            File myFile = new File(startDoc);
            PDDocument pdDoc = PDDocument.load(myFile);
            PDDocumentCatalog pdCatalog = pdDoc.getDocumentCatalog();
            PDAcroForm pdAcroForm = pdCatalog.getAcroForm();

            if (pdAcroForm != null) {
                pdAcroForm.setNeedAppearances(true);
                pdAcroForm.flatten();
            }