Meta query with ACF relationship field

Based on https://stackoverflow.com/questions/42011047/wordpress-query-by-acf-relationship-field, I was able to fix this by changing the 'compare' => 'IN' to 'compare' => 'LIKE'. So the resultant code looks like this:

$new_query_args = [
    'meta_query' => [
        [
            'key'     => 'af_author',
            'value'   => get_the_ID(),
            'compare' => 'LIKE',
        ]
    ]
];

$query_args = array_merge( $query_args, $new_query_args );

I’m not exactly sure why this works, but it fixed the problem.