Drupal Community Portal

Hello,
our website is running Acquia Drupal 1.2.40 (Drupal Pressflow 6.22 core) and the security update to version: 1.2.41 (Drupal 6.24 core) (2012-Feb-02) needs to be done.
Would you please advice me what is the correct procedure in updating Drupal Acquia with Pressflow core?
What I have read on internet (and also have been doing so far) was to rewrite Drupal Acquia files with Drupal Pressflow. As far as I know they should be identical, however Drupal Acquia has extra folder in modules/acquai, which is to be preserved.
Thank you for your advice
Kamil