We have had a large number of users reporting problems with episodes on NPR podcasts disappearing and then re-appearing. This will cause an episode that you have already listened to and flagged as done to re-appear later as new and a re-download to occur.
We have identified the cause to be a problem with the publisher's feed and unfortunately there isn't a way for us to workaround this. In the cast we investigated, (NPR Wait, wait, don't tell - 4/11/14 15:00), the most recent episode is removed from the feed, and then added a few hours later (18:00). This causes DC to remove the episode and then add it later as new.
The only way we can think of to minimize the effect of this is to decrease your feed update interval to the greatest time you can tolerate, since this problem will only occur if a feed update occurs during the timeframe when the feed is incorrect. If your update skips over that, then you'll be ok.
Wish there was better news. I do suggest that users contact the publisher directly to get the issue resolved.
If anyone from NPR would like more details about what we've found, please don't hesitate to contact us.