The theory of Yui disappearing/being replaced is quite intriguing, especially when considering the potential drama of how Asuna would react to it. It would be interesting if Fujino addressed this, but it’s unlikely, just like other themes in the story. Take Liz’s rape, for example, she brushes it off as an inconvenience instead of acknowledging the gravity of the situation. If Liz were acting in character, even in the way Fujino portrays her, she would have called the police immediately upon realizing she had lost control over Inoda. She would have continued without him, because if he was capable of that, who knows what else he might do?
But for plot convenience, she’s just annoyed and seeks vengeance, which doesn’t seem like a true reflection of her character to me, especially considering Kirito’s role. A similar situation might unfold here with Asuna, perhaps Fujino will acknowledge it with a small line of dialogue, but it’s unlikely to play a major role in the plot, which... fair enough. It’s NSFW content after all, but Part 1 showed that the story could have handled it with a bit more creativity.