Geralt himself mentioned that his feelings and memories were linked, so we can expect that his feelings for Yen have returned. The fact is, however, that Geralt (might have) had time to get involved with Triss during his amnesia, but there's also the fact that Triss never once mentioned Yennefer's existence to him, so he probably feels betrayed by her.
The situation is rife with potential for storytelling, and what's the point of playing the game if not for the storytelling. It's not just that you want to see events unfold in a story-based RPG, but that you want to actively affect them; so, it would make the most sense to let players stay in control of the Yen storyline.
I mean, let's be honest- the Yen storyline is the main storyline of the game, and I just hate the idea that the main storyline of the game is going to be static, linear, and unaffected by player involvement; it just wouldn't make sense as a choice and consequence RPG to neglect giving players a choice in the main storyline of the game.
An amnesiac (might have gotten/) got involved with someone during the course of the games, that's why there's the possibility that even though he got his memories/feelings back, he might be conflicted.
It doesn't matter what Geralt chose in the past (applies to both Triss and Yen) when he's equally capable of choosing two different routes now. No one else but the player should decide which route he chooses because we're the ones playing the game, otherwise, why don't we just watch a movie.
So basically, it doesn't make sense for a story-based choice and consequence game to not let you make a choice in the most important plotline of the game, and it doesn't make sense for anyone other than the player to make role-playing decisions during the course of the game. Again, what's the point of playing the game if not for the storytelling and the choicing and the consequencing.
...I have more to say (sorry).
I also don't understand why it would affect other players what someone else does in their own game. If you're worried about the integrity of Sapkowski's work, then you're a bit late on that- an adaptation of a work has no obligation or necessity to follow the course of the original work to the letter (sorry); in fact, doing so would be counter-intuitive to the act of adapting something.
I don't think we should think of Geralt as a lesser Geralt if he does something which you believe book-Geralt might not do- his actions during the course of the games have changed him as a person, and it makes sense for the games to acknowledge that fact, otherwise what was the point of this journey?
The storytelling which occurred during the games was just as potent and meaningful a journey as that which occurred during the books, and the length of time doesn't matter because Geralt was an amnesiac when he acquired new experiences; we can expect that those experiences affected him greatly because of his almost "blank" state. That's why it's certainly possible for Geralt to be conflicted about his feelings in TW3, despite regaining his memories.
Moreover, Geralt and Yen ending up together no matter what is just too clean and fairytale-like, I mean that it's so expected. If I already know the ending of a story-based game, and I'm playing it for the story and choices, then why should I play it. Why should Geralt choose Yen? Because books? Because fuck the players? These reasons are not justifiable for an evocative story-based choice and consequence role-playing game; if these words mean anything, then these reasons don't apply.
...that's everything, okay. Have fun and bye