hi thanks for the reply. i ended up doing it another way. i was updating a site that was on Joomla 1.7. So I ended up leaving Joomsef for last.
Once the site was updated to 2.5, I used the update tool in joomla to try and update joomsef. I got a message saying that it is an invalid component and it disappeared from the components dropdown menu.
After a brief panic I checked in the extensions manager and saw that joomsef is still installed. So then I merely tried installing it again through Joomla's extension manager and, boom, it worked.
Joomsef working again and updated to latest version and, thank the joomla gods, i did not lose my urls or config again!