Apple really screwed up on this one. There appears to be a major issue with the AppleTV software version 3.0 that can potentially cause your media to disappear after a while. If you have AppleTV software version 3.0, you should restart your AppleTV and upgrade to version 3.0.1.
Apple is saying the symptom of the issue caused by version 3.0 is:
“You are using Apple TV software version 3.0 and all of your movies, TV shows, and songs appear to be missing,”
Wow… via Tuaw