Sometimes it will clear everything off and sometimes just most of it. Driving me freaking crazy because everything is wireless in my house and I have to bust out the ethernet cables otherwise its sooooo slow. Any ideas why this is happening?
If that's the case then I think you either have a hardware problem on the Apple TV OR somehow the Apple TV is linking with another iTunes Library which would cause all of your content to be deleted and be replaced by whatever is in the other iTunes Library. Of course, if this happens and then the sync from the second library is interrupted it would be possibly for only a few or zero items to be copied back to the Apple TV.
While you can stream from multiple PCs to one Apple TV you can only COPY contents to the Apple TV from a single iTunes Library.