Upgrading from 6.x-2.0-beta23 to 6.x-3.4

So, Drupal told me that I need to update to your latest version of Pathologic. However, when I did it updated the database and I know longer had functionality to change the path of /drupal/xx to simply /xx. Since so much of my site rest on this I am, I can't update it until I am assured that this will work. Last time I updated, I had to quickly restore my database and downgrade to 6.x-2.0-beta23