An update for Apple TV was released Saturday which fixes problems with content disappearing from the system until re-syncing.
Apple suggests that users who have updated to the 3.0 version should immediately update to version 3.0.1 in order to prevent content from temporarily disappearing until re-syncing.
The Apple TV should be restarted and updated through the “update software” option under the Settings > General menu. If this does not resolve the issue, it is recommended that the Apple TV be disconnected and reconnected to the computer that it is networked with.
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