I contacted support and was able to resolve the issue. What I needed to reference was the api-value.php file starting from line 293 in the plugin folder. This pointed me to how I can target the specific field name to make the footnotes work. Updated code (changes in bold):
add_filter(‘acf/format_value/name=publication_content‘, ‘format_value_wysiwyg’, 10, 3);
function format_value_wysiwyg( $value, $post_id, $field )
{
$value = apply_filters( ‘the_content’, $value );
return $value;
}
