So, something more concrete as to what was added to the final product rather than removed/changed, that scene was definitely part of the reshoots: http://collider.com/rogue-one-darth-vader-scene/
Speculation:
Given that the Vader scene at the end was part of the reshoots, maybe there was an earlier version of the ending which didn’t cause continuity problems with ANH i.e “Where are those transmissions you intercepted?”, “We intercepted no transmissions. This is a consular ship. We’re on a diplomatic mission.”,“Several transmissions were beamed to this ship by Rebel spies”. Although this is all kind of true of Rogue One, the way the Captain and Leia try to pretend they are on a diplomatic mission when Vader just personally chased them out of a docking bay doesn’t really work, and why would they go directly from the battle to Tatooine. “My mission to bring you to Alderaan has failed”, well why did you try and do it with a Star destroyer in hot pursuit?
Maybe there was once a version where Leia really was on her mission to pick up Obi-wan, and either the Rebel Fleet relayed the plans to her, or the spies on the ground sent the plans directly to them rather than to the fleet, this may account for the re-positioning of the communication dish, the reason for which wasn’t really explained in the film.