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I've got my sections working, with:

  #Landscape section - Next Page
  $landscape_fragment = new Phpdocx\Elements\WordFragment($docx);
  $landscape_fragment->addWordML('<w:p xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"><w:pPr><w:sectPr><w:type w:val="nextPage"/><w:pgSz w:code="9" w:h="11906" w:orient="landscape" w:w="16838"/><w:pgMar w:bottom="850" w:footer="708" w:gutter="0" w:header="708" w:left="1077" w:right="1077" w:top="850"/><w:cols w:num="1" w:space="708"/><w:docGrid w:linePitch="360"/></w:sectPr></w:pPr></w:p>');
  $landscape = '<phpdocx_wordfragment data-content="'.base64_encode(serialize($landscape_fragment)).'" />';
  $variables['landscape'] = $landscape;

  #Portrait section - Next Page
  $portrait_fragment = new Phpdocx\Elements\WordFragment($docx);
  $portrait_fragment->addWordML('<w:p xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"><w:pPr><w:sectPr><w:type w:val="nextPage"/><w:pgSz w:code="9" w:h="16838" w:orient="portrait" w:w="11906"/><w:pgMar w:bottom="850" w:footer="708" w:gutter="0" w:header="708" w:left="1077" w:right="1077" w:top="850"/><w:cols w:num="1" w:space="708"/><w:docGrid w:linePitch="360"/></w:sectPr></w:pPr></w:p>');
  $portrait = '<phpdocx_wordfragment data-content="'.base64_encode(serialize($portrait_fragment)).'" />';
  $variables['portrait'] = $portrait;

However, I'm losing my footer; which was being added by:

<phpdocx_footer>
    <div class="print-footer">
        <table border="-" style="border-collapse: collapse; width:100%;">
            <tbody>
                <tr>
                    <td class="text-left font-8"><phpdocx_pagenumber data-target="defaultFooter" data-type="numerical" data-fontSize="8" data-font="Open Sans" data-textAlign="left" /></td>
                    <td class="text-right font-8">
                        Pearson BTEC Levels 4 and 5 Higher Nationals in {{ subject }}<br/>
                        Specification - Issue {{ issue }} - {{ issmonth }} {{ issyear }} &copy; 2019
                    </td>
                </tr>
            </tbody>
        </table>
    </div>
</phpdocx_footer>

I'm assuming that I need to have footers defined as part of my sections. Is this correct?