Hello,
UPDATE: phpdocx 13.5 added support for this specific style when merging documents.
Thanks for sending the requested documents. The issue is a not supported style when applying override numberings that appear multiple times with the same ID; the current testing branch of phpdocx includes support for this case (all users with the latest version of phpdocx can request this update to add support for this specific case sending an email to contact[at]phpdocx.com).
We have sent to your email the updated class.
Regards.