I finally had the chance to rewatch the last episode. I also went back to the first 2 episodes just to see the scenes of the "current" Bernard, the one that woke up on the beach. There have really only been 3 scenes with him so far and he says very little.
Ep1, he wakes up on the beach, clearly confused. He recognizes the guy saying "shoot a woman, over my dead body", seemingly remembering that he programmed him to be virtuous. He then questions Strand about executing hosts, saying that some of them aren't hostile and tells them it is Dolores in the video killing the GN guy they took the brain out of. At the end of the episode, he sees Ford dead and then at the lake, while clearly fixated on a floating dead Teddy says that he killed them all.
He doesn't appear in Ep2
In EP3, Charlotte asks him "Do you have any idea where Peter Abernathy might have gone?. He seems to keep slipping away from us"
That's it. Those are the only scenes with current Bernard. The last time we saw him before waking at the beach was for some reason Clementine knocked him out and dragged him away. Charlotte somehow loses Abernathy from when they drive him away from the fort to when she questions Bernard underground. Maybe not the physical body of him but the data stored. They might realize he's been drained of the data once they get him to safety. Rewatching the scene where Bernard is with Abernathy during the attack, it isn't as obvious as I first thought that he uploaded the data into himself but maybe he could store it in the tablet to transfer it later? I don't know. Definitely seems like he has the data somehow though.
One other interesting thing was Dolores telling Teddy to go back to Sweetwater with her, saying "There's something I need there" It explains why she appeared in the video taken from the GN brain, which was dated 11 days and 9 hours from when they watched it. It falls in that timeline I guess. And if GN is there to protect humans, it makes sense that they would be where they were, and why hosts had arrows in them. GN was part of a counter to the rebellion. Hmmm...still need to know how Stubbs is alive. He hasn't said much. Not sure what Dolores would need at Sweetwater though.