stop-date-modified-update.php

<?php
function stop_modified_date_update( $new, $old ) {
    $new['post_modified'] = $old['post_modified'];
    $new['post_modified_gmt'] = $old['post_modified_gmt'];
    return $new;
}

add_filter( 'wp_insert_post_data', 'stop_modified_date_update', 10, 2 );

// do stuff that updates post(s) here

remove_filter( 'wp_insert_post_data', 'stop_modified_date_update', 10, 2 );

This gist shows how to disable/enable WordPress' update of the post_modified and post_modified_gmt fields.