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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.
I had the same problem and fixed it by looking into the docx library.
In phpdocx\classes\MultiMerge.inc there is an foreach loop for $documentArray as $key => $secondDocument.
In this loop each file is opened, but never closed.
So I added the following line "$this->_secondDocx->close();" at the end of the loop, and the last file in the array was deleted when using the unlink function.