Core update procedure for OpenPublish

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).
Notice: Undefined index: sidebar_second in include() (line 144 of C:\wamp\www\example.net.au\openpublish\modules\system\page.tpl.php).

Then when I go online it seems that OpenPublish has lost track of the theme and stylesheets and the following warnings appear:

Notice: Undefined index: highlighted in include() (line 126 of C:\wamp\www\example.net.au\openpublish\modules\system\page.tpl.php).
Notice: Trying to get property of non-object in _theme_load_registry() (line 318 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Undefined index: sidebar_first in include() (line 138 of C:\wamp\www\example.net.au\openpublish\modules\system\page.tpl.php).
Notice: Undefined index: sidebar_second in include() (line 144 of C:\wamp\www\example.net.au\openpublish\modules\system\page.tpl.php).
Notice: Undefined index: gazette in drupal_theme_initialize() (line 100 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Trying to get property of non-object in _drupal_theme_initialize() (line 145 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Undefined index: gazette in _overlay_region_list() (line 795 of C:\wamp\www\example.net.au\openpublish\modules\overlay\overlay.module).
Notice: Undefined index: gazette in _overlay_region_list() (line 795 of C:\wamp\www\example.net.au\openpublish\modules\overlay\overlay.module).
Notice: Undefined index: gazette in drupal_theme_initialize() (line 100 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Trying to get property of non-object in _drupal_theme_initialize() (line 145 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Undefined index: gazette in _overlay_region_list() (line 795 of C:\wamp\www\example.net.au\openpublish\modules\overlay\overlay.module).
Notice: Trying to get property of non-object in _theme_load_registry() (line 334 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Undefined index: gazette in theme_get_setting() (line 1414 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Trying to get property of non-object in theme_get_setting() (line 1451 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).
Notice: Trying to get property of non-object in theme_get_setting() (line 1461 of C:\wamp\www\example.net.au\openpublish\includes\theme.inc).

Any thoughts on what I am doing wrong here with the core update of Drupal 7 within OpenPublish?