I think your memory loss theory is interesting, but there's really no evidence for it in the film.
After being burned, John resumes his obsessive hunt for the Fizzle Bomber. But I suppose the Bureau could have filled him in, had him listen to the tape recording, look through John's case files, told him he's been chasing the FB for years, etc. As you say, he'd still be pretending surprise in the bar at the case details, but the dialogue would flow organically instead. We do see John and Jane having conversations that John would surely remember having from the other side, so it's not like he doesn't have experience recreating conversations, even if he remembers them.
I do think Barkeep remembers his life as Jane and John. Barkeep claims to John that he also loves Jane, but was it just a line the Bureau fed him for some inexplicable reason (seems unnecessary to the mission)? He also seems to remember the hurt when Baby Jane was kidnapped, causing him some internal struggle before Robertson comes to keep him on task.
Still, an interesting thought.
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