I've seen a few reviews of the DVDs that say Palpatine's new dialogue in ESB SE 2.0 completely negates the Expanded Universe stories that explain how Vader finds out about Luke's identity.
Luke and Vader only met up twice that I can think of between ANH and ESB, in Vader's Quest and in Splinter of the Mind's Eye.
Vader's Quest is hardly the shining moment of SW comics. Overall, it's pretty mediocre, but with a few great scenes (like Vader losing his temper and using a Stormtrooper's rifle to incinerate everything around when he first hears "Skywalker" used to describe the pilot who destroyed the Death Star). The Vader/Luke matchup here is very brief (and ridiculous), and there are tons of bystanders. Not the time or place to announce your proposal for what boils down to high treason.
The final scene shows the Emperor in his throne room, discussing with a spy how he suspects Vader knows Luke's identity and wants to keep the knowledge from Palpatine.
No problems there. If Vader's trying to keep a secret, he's not going to suddenly say, when he learns the Emperor knows, "Okay, boss, you got me. Good one! My mouth was open!" He's going to lie and play dumb.
In Splinter of the Mind's Eye, Vader actually speaks briefly with Luke, stating that he expended a lot of resources to learn his identity (but, being written prior to ESB, obviously doesn't say anything about his own connection to Luke). Luke gets incredibly lucky in a duel, slicing off Vader's often-amputated right arm and knocking him into a pit.
So Vader didn't have a chance to tell Luke, and possibly didn't want to with Leia (who he doesn't know about at this point) present.
And then in the scenes of ESB leading up to his conference with Palpatine, there's no question at all that he knows who Luke is. And that he plans to keep telling Palpatine that he's after the Rebel Alliance, not specifically Luke.
It's been "known" in the EU for a long time that Vader is lying to Palpatine about the extent of his knowledge and his plans. It's also been "known" that Palpatine is fully aware of this and allows it to continue. And putting the prequels together with ROTJ, it's pretty clear that both Vader and Palpatine want to turn Luke into the next Sith Apprentice at the expense of the other's life.
So what's the supposed problem? I prefer the original dialogue, but I can't see this glaring continuity error that's supposedly there? Am I just missing something?