I've noticed that in recent versions (definitely 2.1.0, not sure about prior versions), deleted episodes remain in the playlist. The episodes are deleted and marked as such, but stay at the top of the playlist.
If I change views and later go back to the playlist, it seems that this act of refreshing the playlist view removes the deleted episodes.
This does not happen all of the time, and it seems that PT is occasionally cleaning up the playlist, although I'm not certain on this point.
I also mentioned this in the "Feature Requests" forum in this post: viewtopic.php?f=4&t=440#p2375