Hello,
What type of comments are added to the DOCX? commentExtended types from new versions of MS Word are supported since phpdocx 9.5 (https://www.phpdocx.com/news/post/phpdocx-v9-5-release-notes/219).
You are using an Advanced 6.5 license, you can use DOCXPath to remove specific Word contents in the document using removeWordContent (https://www.phpdocx.com/api-documentation/docx-path/remove-elements-in-docx). If you send to contact[at]phpdocx.com two DOCX samples that return the error when merging with phpdocx 6.5 we'll check them.
Regards.