It is possible to disable individual e-mail templates and e-mails, associated with won't be sent out. This is true in most cases, however in case if same e-mail template is used twice-in-a-row or more times, then 2nd and other e-mails will be still sent out regardless of e-mail template status.
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Error rendering macro 'jira' : Unable to locate Jira server for this macro. It may be due to Application Link configuration.