How do I stop trusting an individual workbook/document in Excel?

OK I've solved it myself. The key was realising that when I renamed the file the trust was lost. Simply open regedit and navigate to HKEY_CURRENT_USER\SOFTWARE\Microsoft\Office\16.0\Excel\Security\Trusted Documents\TrustRecords. Delete the entry for the document you no longer trust and voila! the document will no longer be trusted. If your version of Office is different or the Application you are dealing with is not Excel (e.g. Word, Powerpoint, Access or Visio) then the registry path will be slightly different but should be easy to find.

I found the following pages were useful references on trusted documents in the registry although none of them contained the actual answer:

  • https://social.msdn.microsoft.com/Forums/en-US/d0a4090f-9ac8-41c6-9e9c-95c2ef0c247a/trusted-document-set-via-registry
    • https://social.msdn.microsoft.com/Forums/office/en-US/b500c52e-43e1-4e52-a8e9-464380cb252f/access-2010-is-there-a-visible-trusted-documents-list
    • https://blogs.technet.microsoft.com/office2010/2009/09/28/trusted-documents/