That's why we use an LDAP user directory. We change the email from the active directory where the actual email adresses are assigned to users, so the changes take place automatically.
But if I had to do change emails on internal directory users, I would use the JIRA CLI plugin.
You can run a script in the language you like and feed it your list of usernames and emails.
Of course, scriptrunner is also good, and has other very useful applications.
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