Custom post type blog pagination conflict

Thank you to Milo for pointing me to the pre_get_posts hook. That was exactly what I needed.

Here is my updated code:

Archive page code

<?php
   get_header(); 
   get_template_part( 'include/content', 'head' );
?>

<div class="postcontent nobottommargin<?php if( semi_option( 'blog_sidebar' ) == 'left' ) { echo ' col_last'; } ?> clearfix">
<?php
        if ( have_posts() ) :
        ?>
        <div id="posts" class="small-posts clearfix">
        <?php
            while ( have_posts() ) : the_post();
            ?>

                            <div id="post-<?php the_ID(); ?>" <?php post_class('entry clearfix'); ?>>
                                <?php
                                get_template_part( 'include/blog/casestudies/post', 'standard' );
                                ?>
                            </div>
            <?php                
            endwhile;
            get_template_part( 'include/blog/navigation' );
            ?></div><?php
        else :
            get_template_part( 'include/blog/error' );
        endif;
        ?>
</div>
<?php
get_sidebar('casestudies');
get_template_part( 'include/content', 'foot' ); 
get_footer();
?>

I then added this to functions.php from the codex

function hwl_home_pagesize( $query ) {


    if ( is_post_type_archive( 'emp_case-studies' ) ) {
        $query->set( 'posts_per_page', 5 );
        return;
    }
}
add_action( 'pre_get_posts', 'hwl_home_pagesize', 1 );