Editing a custom user field onBeforeSave
Solution:

Instead of:

$user-&gt;fields['notificationAlreadySent'] = '1';


Use

$user-&gt;getContent()-&gt;setAttributes(array(
    'notificationAlreadySent' =&gt; 1
));


Of note: I find this sort of thing extremely hard to research. I know what I want to do (edit the value of a field in an event via the onBefore listener) but documentation on how to do that seems non-existent. I keep finding this sort of problem with developing Craft plugins - that unless you know the internals, you're really hard pressed to even articulate what you're wanting to search for in order to find a solution.