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Scene where Lloyd first meets Yuan:



Lloyd: Phew, that was close.
Yuan: And just who the hell are you?
*Yuan gets ready to blast Lloyd*
Lloyd: Give me your name, and I shall give you mine!
Yuan: Hahaha! You certainly have guts. But I’m afraid I don’t see the need to introduce myself to a miserable little creature like you.
Lloyd: What a coincidence, cause I don’t see a need to introduce myself either to a moron who doesn’t realize how pathetic he is.
Yuan: Why you little!...
*Lloyd holds up his arm to block Yuan’s attack, Yuan notices his exsphere and shocked*
Yuan: An exsphere! You’re...Lloyd?!
Lloyd: And if I am?
Yuan: Hmm, I see the resemblance.
*Lloyd gets out his sword and is ready to attack, Yuan backs away*
*Botta enters, Yuan and Lloyd move about*
Botta: Sir! We’ve received reports that the Chosen’s group has infiltrated the facility!
Lloyd: You...you’re the Desian that attacked Iselia!
Botta: So you’re Lloyd! Now this is amusing!
Yuan: Botta! I’m leaving for now. Are plans will be ruined if he sees me.
Botta: What of the Chosen?
Yuan: I’ll leave that to you.
Botta: Understood.
Yuan: Lloyd. The next time we meet, you’re mine. Just you wait.
*Botta corners Lloyd, the Chosen’s group walks in*
Genis: Lloyd! Are you okay?
Colette: Are you all right? Are you hurt?
Kratos: He looks find.
Lloyd: You guys all came for me?
Botta: Perfect timing. I’ll take care of everyone at once!
Kratos: Get ready.

Scene at Altessa’s house



Lloyd: !! My body...I can’t move.
*Yuan is paralyzing him with magic*
Yuan: ...Do you like to meet your father?
Lloyd !! What have you done with my dad?!
*Yuan teleports outside, Lloyd sits up*
*Lloyd exits Altessa’s house, Yuan’s men hold their swords up*
Lloyd: ...Kratos! The Renegades and Cruxis are enemies, aren’t they?! So why?...
Yuan: Quite. ...Of course, the drug should have everyone sleeping soundly.
Lloyd: Drug?! ...Where’s my dad? If you’ve done anything to my dad. I’ll tear every last one of you to pieces!
Yuan: Now, now, is that the way to act when you’re about to meet your father for the first time?
Kratos: So it was you, you were the assassin you tried to kill me at Hima.
Yuan: Kratos. If you value your son’s life at all, do as we say.
Lloyd: What are you... talking about?
Yuan: Release Origin’s seal. Otherwise, Lloyd will die right here.
Lloyd: No...Kratos can’t be my dad. I c...I can’t believe that....I won’t believe that!
Yuan: How does it feel to have your own son reject you like that?
Kratos: ...Humph.
Yuan: ...I’d guess from your attitude that you don’t plan on releasing Origin....If that’s the way it’s going to be, then you’ll just have to die!
*Yuan’s men go closer to Lloyd*
Lloyd: Ugh!!
Kratos: (!)
Yuan’s men: One move, and your son dies!
Yuan: You changed when you got a family. Just like that time fifteen years ago. When Anna turned into a monster, you lost your ability to fight back.
Lloyd: (!) ...What?
Yuan: If she hadn’t been together with you, she would of never turn out like that. Such an unfortunate women.
*Lloyd walks forward and gets knocked down then gets up*
Lloyd: Don’t mock my mom!
*Lloyd attacks Yuan, Yuan dodges and attacks Lloyd, Kratos takes the blow*
Lloyd: ...Kratos?
Kratos: ....Are you alright? ...Good.
*Kratos falls back*

//Lloyd freaks out then there’s that long scene with Colette//
//Then a long scene with Mithos//

Afterwards when you talk to Yuan:

Lloyd: ...Are you all right?
Yuan: With this, all of our efforts have been rendered useless....
Lloyd: You planned to form the pact with Origin and use the Eternal Sword.
Yuan: Correct. And then, we would use the Mana Cannon to destroy that infernal tower. Allowing the Great Seed to sprout. That was out plan. Upon learning of your existence form a Desian insider, I was certain I would be able to force Kratos to participate.
Lloyd: You...didn’t approve of Mithos’ Age of Half-elves?
Yuan: That plan was the result of a twisted perception of Martel’s last wish. It’s not what she truly desired.
Colette: What was Martel’s last wish?
Yuan: She said she wanted to see a world free from discrimination.
*Lloyd shakes his head, Yuan stands up*
Lloyd: You shouldn’t move.
Yuan: No. There’s no time. I must evacuate the Renegades before they are killed by Yggdrasill.
Lloyd: Wait. Is Kratos really the only one who can release Origin’s seal?
Yuan: Yes. The seal will be released upon freeing the mana from his body.
Regal: If he does that, he’s likely to lose his life.
Yuan: Yes. The seal is based on his own life.
Lloyd: (!) Kratos’ ...life... Are you saying we have to trade his life in order to get the Eternal Sword?!
Yuan: ...Lloyd. You won’t be able to use the Eternal Sword. It does not require the power of a summoner. You must merely be acknowledged by Origin. However, there is one thing you cannot do anything about.
Lloyd: What do you mean? Yggdrasill...Mithos said that, too.
Yuan: Only half-elves can wield it. That sword was created by Origin for Mithos.
Lloyd: ...What?!

Well, I'm assuming that Yuan and Kratos would be pretty good buddies, considering that they first went with Mithos in the first place, and saved Kratos by giving him mana. Wouldn't Yuan probably know about everything?

Notice he said he learned of his existance, not explicitly his heritage. It could mean that he learned of Lloyd's plan or location.

And he could be speaking of his resemblance to either. It never tells us how long Yuan has been going against Yggdrasill, or if he even was with his cause after the war anyway. (Though I'm assuming he was...)

If he dug deep enough, Yuan could have probably found out everything if he wanted to.

So, my conclusion is that Yuan knew everything the whole time.

We all love Forcy. mrgreen xd