In the Zotero tab, click "Unlink citations" (or "Remove field codes" on older versions of the Zotero plugin). This will convert all of the Zotero fields into plain text. This is a permanent change, so save a copy before you do this. I would probably recommend unlinking the citations, saving it as a new document, then deleting everything by the bibliography to make comments on (make you other comments on the paper in the original file).