A script upgrade? Sounds like your db upgrade wasn't completed fully. Do you have the original backup of the database? What patches did you apply and what was your original version number?
Can't remember what version but I followed the steps on the older versions to a newer one, one version at the time, I applied all the patches according to the instructions and the database still the same, all previous urls are still there, new ones dont work
You will need to raise a ticket for this. If you haven't completed the upgrade correctly you'll need to revert to your original database and re-apply the db patches.