What templates are you talking about? Some of them are dynamic (a refresh of the browser will render the changes immediately) and some of them are static (a server restart is needed). So it depends on what templates are you talking about.
For the static ones, you can get some odd behaviour, but you can edit them while JIRA is running without running the risk of data damage. As Gabrielle says, you will need a restart to get JIRA to notice your changes.
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