Hello,
To accomplish that task you need to use the MultiMerge method available in Corporate and Enterprise licenses. Phpdocx shares headers and footers for all sections, so you'd need to create two documents and then merge them using this method:
http://www.phpdocx.com/api-documentation/docxutilities/merge-Word-documents-with-PHP
As you canse there's an option to continue or restart numbering.
Regards.