I always assumed that Obi Wan knew who Vader was the whole time. He had gotten to a point psychologically where he referred to both himself and Vader as new people, with the previous personas dead. Hence that "Obi won Kenobi? There's a name I haven't heard....." line.
Wouldn't it have been common knowledge that Vader was Anakin? Otherwise you'd have to assume that the Emperor just had some other ultra powerful force just apprentice instantly, who also had a much of robot parts and a breathing machine.
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