Apple warns its customers that the 3.0 version has some bug which makes data disappear temporarily. Apple has also suggested stepwise procedure for the issue and there are chances that the problem may still persist after the upgrade so they further suggest to try after disconnecting and reconnecting the systems.

The procedural step includes:

Restarting the Apple TV, then after selecting setting under General from Main menu choose update software and download it to install.

If the issue as Apple states “Apple TV software version 3.0 can possibly cause your content to disappear after a period of time.” Still persist Apple suggest to try disconnecting Apple TV from your computer, and then connecting it again.

To disconnect and then reconnect a computer steps suggested are as follows:
1. On your Apple TV, go to Settings > Computers.
2. Select your iTunes library to disconnect.
3. Select your iTunes library again to reconnect.

Apple support over the issue regarding re-syncing can be found out at Apple support center.