Is video sync broken?

Since the last couple of weeks, I've had problems watching my videos between my ipad and apple tv. I've not tried iTunes itself mostly because I'm afraid of messing the whole thing up. My iPad and ATV get confused about if I've watched the video, or part of the video. If I sign out of iTunes and sign back in, all of the videos disappear. I thought about signing out and back in when a new TV season wouldn't show up. Restoring the iPad worked the last time, however I do not want to restore the iPad every other couple of days. Is there a solution to my problem?