Citations may get unlinked when copying and pasting sections of the document if you do not have the Zotero Connector installed, or if you have collaborators on the document and they don't have it installed. There were some bugs in the Connector that could have caused copying to unlink citations, but they have been fixed for over a month now. If you have the Connector installed, try to monitor whether citations get unlinked when copy-pasting text and if they do please post with the specifics of what you did and what happened.