[user104658]

Originally Posted by Jarrod

The memory thing could be something as simple as the time streams correcting, like in the 50th - how the 10th Doctor wouldn't remember what had happened

True - and it was made pretty clear that the latest doctor in the time stream (Matt Smith at that point) would remember while 10th and the "war doctor" would forget. However Missy doesn't just not remember the things from where the two masters encounter each other... She doesn't seem to remember anything about the ship at all, even though it seems the master has been there for decades if not hundreds of years...