How do I empty a specific meta_value for all users in PHP

You could specify the meta key in the user query so the results you’re getting back are only for users who have an existing field.

For reference WP_User_Query custom field(user meta) params.

$args = array(
    'role' => 'Subscriber',
    'meta_query' => array(
        array(
            'key' => 'old_meta_key_name',
            'compare' => 'EXISTS'
        )
    ),
);
$users_with_meta = new WP_User_Query( $args );
$users = $users_with_meta->get_results();