Then open existing docx document as XWPFDocument, On onDocumentRead method  initFootnotes method dublicate existing Footnotes in document.

Here is a sample code with comments where there is a duplication:

private void initFootnotes() throws XmlException, IOException {
       for(POIXMLDocumentPart p : getRelations()){
          String relation = p.getPackageRelationship().getRelationshipType();
          if (relation.equals(XWPFRelation.FOOTNOTE.getRelation())) {
             FootnotesDocument footnotesDocument = FootnotesDocument.Factory.parse(p.getPackagePart().getInputStream());
             this.footnotes = (XWPFFootnotes)p;
             this.footnotes.onDocumentRead();      // THERE ARE WE ALREADY HAVE XWPFFootnotes WITH ALL DOCUMENT FOOTNOTES

             for(CTFtnEdn ctFtnEdn : footnotesDocument.getFootnotes().getFootnoteList()) {
                footnotes.addFootnote(ctFtnEdn);   // THERE ARE FOOTNOTES IS DUBLICATING
             }
          } else if (relation.equals(XWPFRelation.ENDNOTE.getRelation())){
             EndnotesDocument endnotesDocument = EndnotesDocument.Factory.parse(p.getPackagePart().getInputStream());

             for(CTFtnEdn ctFtnEdn : endnotesDocument.getEndnotes().getEndnoteList()) {
                endnotes.put(ctFtnEdn.getId().intValue(), new XWPFFootnote(this, ctFtnEdn));
             }
          }
       }
    }