I have beat "Atonement" throughout (killed John after plane fight). See journal below showing the game registers I've beat the mission.
However, the map still prompts me to go to Fall's End in order to meet John (which, obviously, I have already done).
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Hey W1llsk1,
Thank you for the screenshots and information! I'm really sorry this is happening, and I will forward this information to the devs.
Any updates will be posted on the forum, however please try loading an earlier save as a workaround. You may need to restart the game if this does not work, however.