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Back in The End of Time, the time-locked Gallifrey was temporarily returned by the Master. But since the Day of the Doctor changed this into Gallifrey being
hidden in another universe, as the Time of Doctor revealed,
what will have been happening (no grammar for timey wimey, I'm afraid) to that former plot? In this new timeline the Gallifreyans don't appear to need the Master's assistance to return, but only the "Go" from the Doctor that the Universe is safe for them to return to.
There are two separate, but parallel events going on at close to the same time, if not simultaneously. The President and the Gallifreyan High Council are causing the events in the End of Time with the Master. In Day of the Doctor, the Doctor contacts the War Council (the military leadership) and effects the events of Day of the Doctor.
There is one line in Day of the Doctor that gives this away. Near the beginning, during the Fall of Aracadia events, Androgar (the aide) mentions that the High Council was in emergency session, that they have "plans of their own". The general replies "To hell with the High Council. Their plans have already failed."
Now it isn't clear whether the events of the End of Time are the "plans of their own" or the plans that "have already failed", but it is clear that they are two separate event lines going on at the same time. I don't see that there is any paradox involved at all.
