After installing iTunes 9, iTunes rebuilds your iTunes library. That is not a problem. The gotcha comes when you try to sync an iPod, etc.
iTunes 9 FORGETS YOUR iPod SYNC SETTINGS and changes them to something else! This can result in erasure of items from the iPod. Recovery requires re-copying items to the iPod and this may take some time for a large capacity device.
Workaround: After connecting your [iPod|iTouch|iPhone], cancel the sync as soon as you can. Review the settings and correct the changes. Then Apply to sync the device.
YES, I did send feedback to Apple, but the feedback form does not know about iTunes 9, so I lied and said I was running iTunes 8.1 and put that in the comments field as well.
I've only connected my touch, but I didn't have a problem. Did the touch/iPhone update too, and everything is the way it should be. I have it set to manual control, with only the apps syncing. Calendars, addresses, etc. are set to sync through my MobileMe account.
"I really need a new tagline"
—P M Evans
Video iPod - synced directly by iTunes.
The movies, etc., sync changed from "all" to "all unplayed". This removed many items.