Hello,
The methods addExternalFile and replaceVariableByExternalFile use an altChunk tag that is not supported by the conversion plugin (this special tag is only supported by MS Word on Windows). Yon can read about this tag on:
http://www.phpdocx.com/documentation/conversion-plugin/common-problems-and-possible-errors
To transform HTML to DOCX and be able to transform the output document to PDF, please use embedHTML or replaceVariableByHtml methods.
If you need to merge DOCX please use the mergeDocx method:
http://www.phpdocx.com/api-documentation/docxutilities/merge-Word-documents-with-PHP
Regards.