MaxSem's answer didn’t work for me, but here is the MediaWiki service script (introduced in v1.27) that will do the trick: https://www.mediawiki.org/wiki/Manual:ResetUserEmail.php
Go to the base directory of your wiki and enter something like this:
php maintenance/resetUserEmail.php uuuu new@email.address
change user email address to new@email.address. By default, this will change the user's password, so the user will have to reset it, which can usually be done on the wiki site. You may need to add a username and password to access the database, for example:
php maintenance/resetUserEmail.php --dbuser myuser --dbpass wordpass uuuu new@email.address
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