Thank you for your response!
So what if a post or term that uses them was added and then the menu was removed?
It was an ACF option page, which basically seemed like a post to me which I could assign custom fields to so if custom fields were added to it and then removed and then the menu was removed in the code would the menu item then stay?
I will also check to see about a cache or some rogue file on the server or something.
