single.php – how to mark current page in the loop

Here’s a rewritten version of your code

<ul id="questions" class="subpage">
<?php 
$current_id = get_the_ID();

$index_query = new WP_Query( array( 'post_type' => 'faq', 'orderby' => 'modified', 'posts_per_page' => '-1', 'order' => 'DESC' ) );
while ( $index_query->have_posts() ) : $index_query->the_post();
    if(get_the_ID() == $current_id)
        echo 'this post has the same ID as the current global one';
    ?>
    <li><a href="https://wordpress.stackexchange.com/questions/71206/<?php the_permalink(); ?>"><?php echo get_field('short_version'); ?> &raquo;</a></li>
<?php endwhile; ?>
</ul>

Please note that on the index.php you can have queries of single post types as well as of archives(depending on your theme). If in case of an archive this will match the first post of that archive only. If you want to match for other types of templates, please see the conditional tags

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