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Such changes are customizations, and will be lost on upgrade unless migrated manually, see (2) for an alternate path.
a) Export your JEMH User Macro definitions to a text file and prefix them to the Jira macros.vm ./atlassian-jira/WEB-INF/classes/templates/email/macros.vm
b) remove from User Macros in JEMH
c) restart Jira
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