Losing the iTunes Authorization is bad

That was not good: after installing iTunes 9, my laptop lost it's authorization for my Apple account. Strange, I did not do anything wrong (I think). The really bad thing is however that subsequently, a sync to the iPhone removes all apps and their settings from the phone. Perhaps I could have done a restore at this point, but iPhone 3.1 was installed while losing the apps, and I did not want to undo that. Reinstalling apps was easy, but all the layouts and settings needed to be re-entered.