core update

My thoughts are that the new Quickstart 3.0 should eventually:

1) support the semi-automatic download of a number of demonstration websites to help learn Drupal (synergy with Drupal Ladder?);
2) provide a better mechanism than the existing Modules installation page for locating a desired module tar.gz link;
3) provide some assistance with upgrading the Drupal core by providing guidance on database backup and migrate;
4) support the concept of optional tool sets to keep the initial download smaller and allow staged learning of tools.

I have successfully updated Drupal core previously by deleting and replacing all folders and files except the 'sites' folder.

I have installed OpenPublish today and tried the same approach with to update Drupal core from 7.16 to 7.17.

When I initiate update.php I get the following warnings:

Notice: Undefined index: highlighted in include() (line 126 of C:\wamp\www\example.net.au\openpublish\modules\system\page.tpl.php).
Notice: Undefined index: sidebar_first in include() (line 138 of C:\wamp\www\example.net.au\openpublish\modules\system\page.tpl.php).