If you've installed the Apple TV 3.0 software update, you should immediately update to version 3.0.1. This prevents content from temporarily disappearing until it is resynced.
To update your Apple TV software:
1. Reboot your Apple TV (unplug the power cord and plug it back in)
2. Select Settings > General from the main menu
3. Select Update Software
4. Select Download and Install
Note: Your Apple TV will conduct a restart, which is followed by the Apple logo and a status bar.
For more information, please refer to this article:
Sadly, it arrived too late. The 3.0 software wiped out all of the content on my Apple TV forcing a resync of my entire library. Since I've recently upgraded the WiFi at the house, this took only several hours instead of a few days as it did when I first loaded it.
The new interface on the 3.0 version of the Apple TV is really quite nice and let's you get to things a lot more quickly.