The OP described this issue perfectly. I took this original post and altered slightly and submitted bug reports to both iTunes and ATV support. I hope you will too if you're having these problems. I won't keep syncing if this continues, I will stream which has another set of annoying issues.
http://www.apple.com/feedback/appletv.html
http://www.apple.com/feedback/itunesapp.html
I just had an issue today where I tried to play a movie (not purchased thus no DRM) and only the audio played, not video. Upon restarting my apple TV...all content except photos (both DRM and DRM free) was removed from the drive. I'll now have to resync everything. I filed a bug report using Apple's bug reporter http://bugreport.apple.com. Likely the bug is a duplicate because I find it hard for apple to be unaware of this issue if so many of us are experiencing it. The apple tv has had syncing issues for ages, I really wish they'd fix things because if they did it would be such an awesome device. These issues are really frustrating!!!