It is always a better idea to manually restore the data in the iPhone during major firmware upgrade (like moving from 2.2 to 3.0) and not restoring it from the backup made in the iTunes. So if you cannot restore the backup from iTunes then will you lose all your data? No as you can manually restore all your data in the iPhone.
Using the same method I was able to restore all my old and saved SMS, Notes, Calendars and Mail Accounts in the new upgraded firmware. What we need is the location where iPhone stores these SMS, Notes etc and an iPhone file explorer.
To backup all your data just follow the following steps
1. Either download the latest iPhone Browser or SSh into the iPhone via WiFi.
2. Now we need to copy the .db (Database) or plist files of the SMS, Notes etc and save with ourselves.
3. These are the locations where the iPhone saves these databases
Call History: /Var/Mobile/Library/CallHistory
4. So after you have saved the DB and plist files, just copy them back to the same location after the upgrade.
Your data will be restored back to the iPhone.