If the underlying template documents are updated whilst a user has an existing ‘live’ questionnaire in FC Documents, will the documents produced from that questionnaire include the updates?

Yes, the system will always use the latest versions of the templates in preview, download and email, regardless of when the questionnaire was started. If those updated templates mean that additional questions need to be answered, questions have been removed or conditions have been changed in the questionnaire, the user will be alerted and advised to review their answers.