How do you fix a content reference that is not visible in portal content and structure?

I migrated a project with Phire from test to production but the menu was missing in the Phire objects. In production the CREF is not visible in portal content and structure but security was able to give access to a user and they can see it with the Navigator. I have migrated that menu since but the CREF is still not visible.

I have tried migrating the CREF again but if I do that then that user doesn't see this in the Navigator anymore and it still isn't in the portal structure and content.

I have tried to manual add the CREF in production but it says it already exists.