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I've run into a related problem today. We do a print edition that goes to bed early, then we update certain pages for e-Edition later. This time we had a wire story on Trump at the top of the front page for print. Then for e-Edition, we moved the Trump story inside to 11A and replaced it on 1A with a late City Council story. 

So this morning, the River of News for 1A shows the Trump story at the top, and the local council system story is at the very bottom. I had thought that if we had our designers delete the Trump story from 1A, including not leaving it on the pasteboard, it wouldn't show up in the RoN, but I guess this isn't the case. I put in a help ticket asking for what the best practice is in this case, but ... maybe there just isn't one?