Please note this is an old forum thread. Information in this post may be out-to-date and/or erroneous.
Every phpdocx version includes new features and improvements. Previously unsupported features may have been added to newer releases, or past issues may have been corrected.
What license and version of phpdocx are you using? The easiest approach is using the MultiMerge class included in Corporate and Enterprise licenses that allow to merge DOCX keeping their own headers and footers.