Looks like apple finally got around to upgrading the Apple TV to support there new found LP format. And in addition to that left a bug in the system that will cause your content to randomly disappear.
But theres a fix if you have not done so already upgrade again to 3.0.1, Apple’s official method for accomplishing this (sent to me via email):
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
I’ve not had the time to thoroughly explore the new updates but what I have seen so far it appears to be a strictly visual update.