Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
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!!!
 
My solution was to turn off auto synch. Not much of a solution, but Apple's silence is deafening on this issue. I've put two service tickets on this problem and they didn't reply to either. They normally get back within a day or so and say they received the request.
 
Okay, I'm off to see if the new 2.4 firmware fixes the DRMed-media deletion issue. My guess is that it will NOT, but maybe I'll be surprised.
 
Glory be, it seems to be fixed in the Apple TV v2.4 firmware! I need to do some more testing but the first two trials indicate that DRMed material is no longer deleted on the Apple TV just because the iTunes application can't connect to the iTunes Store.
 
Can anyone else confirm that this bug has been fixed in the v2.4 firmware? There seem to be multiple issues with content being deleted from the Apple TV, but the one bug which I'm following is easy to duplicate since it only requires that you disconnect your Mac from the internet and then launch the iTunes application with the iTunes auto synch enabled (check box under iTunes -> Preferences -> Apple TV).

The full description for this bug appears in the first post of this thread.
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.