I did include some but I can elaborate and give quotes yeah!
For all the "how would you convinve her to lie," they didn't know what Alecto was, not fully. Mercy expresses doubt she ever had a genetic code, but if they knew, she'd know as a fact either Alecto didn't or any semblance of it was also John's code, being made partly from his own body.
They assume that Harrow's cavalier having Alecto's eyes—eyes so unnaturally gold that they could have belonged to no one else in the universe, to a point that Augustine's first thought was "fuck me backward, she woke up"—must mean they were actually John's eyes, but that isn't true either.
His eyes weren't gold until the earth started channeling power through him. His eyes were brown, and no one has his original eyes anymore. I've seen people argue she rewrote his genetic code, which, I guess isn't outside the realm of possibility? I just think the sun imagery used with John and Alecto is extremely strong so the fact that they look like a solar eclipse makes the possibility that his eyes are technically-still-sunlight-gold and being literally blocked out by Something Else significantly more likely. Either way:
Her body was made partly from his body. IF it has any human genetic code to speak of, it's his genetic code. If Mercy and Augustine knew what Alecto was, they wouldn't have jumped to "their eyes must have swapped, so she must be his cavalier." They would have thought "of course, we should have guessed his eyes used to be the same color as hers since her physical form came from him", which still would have led to "Harrow's cavalier must have been the child we created", but not "John lied to us about Lyctorhood."
And when he describes Anastasia and Samael, he sounds hungover and claims the secret was to do it slower, more methodical, which we later see couldn't have been less the case for him; she was just too big to eat.
We see part of the "she was too big" part in the above screenshot, "Fuck knows what would've happened if I tried to absorb you all the way; I probably would've burnt to death." It wasn't that he had a method to preserve her; it was that he COULDN'T fully eat her, despite trying. Just above that section says more:
And what he'd said about Samael was...
Here Augustine suggests Anastasia nearly cracked "the right way" of doing it (the way that doesn't exist), and John says yes but with those caveats about his tone.
One big thing people don't acknowledge enough about John is he's not even a good liar. The vast majority of the time, he's basically running on Fae Rules; he relies on Technical Truths, misleading truths, and lies of omission, and even with the latter he's about two seconds from spilling his guts at any given time and slips so much. ("If you knew the whole story, you might strike me full in the face instead", "ten thousand years since I've eaten human being and I really did not want an encore", answering honestly that nukes were involved in destroying the First, etc.) My favorite go-to example for a Technical Truth is telling Harrow that G1deon "made a pact with an authority I have no power to gainsay that he would protect me from any danger." Either you can't gainsay yourself or, sure, I can see him promising Pyrrha he'd make her death mean something, either works. "Now it has been put to him that you are that danger." It sure had! It sure had been put to him. By John. He just doesn't say that part but if you stop and think about it who else would have? He clearly doesn't listen to anyone but John. But yeah! Most stuff he says has some truth to it, which is what makes it really fun to pick apart and figure out what angle has the real truth.
But when he does just outright lie, there are patterns to it.
He'll do his best to omit/avoid anything that makes him sound especially Weak or Vulnerable, even if he might gloss over hints. (The racism he endured, the likely queerphobia, problems with the schools he rattled off, etc.)
He will go so far out of his way to avoid putting blame on anyone he cares about, to a point it loops around into being an ego thing, a la "stopping them was on me, you know?" (He informs us M— was at the head of pushing for more time to work out maternity and that the investors brought up maternity as one of the reasons for shutting it down, but he emphasizes they all stood with her and never, ever blames her. He talks about how much the sheer noise and overstimulation of everything was contributing to his breakdown at the end, how it was taking active effort to keep his power from killing everyone just to get some quiet, but shortly after when he touched earth's soul and dissociated about it for a while, he says she kept screaming, and Harrow-as-Alecto asks, "I was?" and he immediately assures her "It wasn't your fault." He always wants to deflect, never wants anything to be his fault, always wants you to know he had to do it, it was the circumstances you know, but he'll take blame before he'll put it on someone close to him. "There can be no forgiveness for those who walked away, just as there can be no forgiveness for me.")
"Guys as careful as me don't have accidents" IS the big lie in that chapter, and might be either or both of the above, either "c'mon, love, we both know I can't just say I wasn't strong enough" and/or refusing to put blame on the earth despite her very much shoving more power into him than he could control without any consent or instructions.
He'll lie if he's backed into enough of a corner about something he really, really doesn't want to admit, which I do think is part of what's going on with his HtN "confession", specifically not wanting to admit the truth about what Alecto was and his part in the end of the world.
Why would she say this if she already knew, if he'd already said his hand was forced, it was for the common good, everything he says In The Dream? It would have rankled, but it didn't, because he never told them.
And, of course, he'll lie when he's also lying to himself. ("What's the difference?" He's God! He shapes the universe and his word is law. If he says it enough, it's basically true, right? (Wrong.)) He tends to struggle or trip over himself when he does. When talking about Samael, he "sounded far-off and confused, like he was hung over." And
He did love Cristabel, so much that the universe is Space Catholic now specifically because of how much she influenced him. John went to an Anglican boarding school, and if G—'s religious-as-hell grandparents had any influence, they were Methodist (as per celebrating White Sunday). The nun was the one pushing for it being a miracle because John had been baptized, omitting that he'd only gone to the Christian music festival for the underage drinking. John didn't believe in the soul until he got desperate. Mercy didn't have to say anything before she did it, but she told him if he looked her in the eyes and she believed him, she'd forgive him, so I think she did believe him (and that hurt worse; he cared so much and let this happen anyway).
He did love them all, he's clung to them this long. And he's locked in by the end here, with the "love you three until the end of time" and all. But he is tripping over himself a bit, stammering. We see him do that elsewhere when he gets thrown off, not necessarily always lying but when he's distressed (and afraid of losing control of a situation or the narrative), like after telling Harrow he would've liked her as a daughter.
And when he talks about why he super definitely wanted Lyctors.
So here's what I was referencing in the other post too about it being the disciples who came up with the idea, and how John was negligent but he didn't lead them into bad results. He saw them pursuing the wrong leads and didn't stop them.
He gives an answer that doesn't line up with what she's saying, and then cuts her off when she tries to question it. There's the stammering here even for stuff that would otherwise flow fine, but also look at what he's saying. Why would you let someone go away, untouchable? But becoming Lyctors made them harder to see, harder to touch. "Needed them to be my hands, my fingers" draws an interesting parallel between the Lyctors and Heralds to an RB, which Augustine describes like fingers to a hand, so in that way, perhaps there's A connection, but it doesn't change that Lyctoral masking works even on him. That's why he didn't know about the lobotomy until he happened to touch Harrow's head very near the damage and then got really upset. And then he jumps from "I loved them too much" to reiterating his crimes against the earth. "I needed my loved ones to be something I could touch" but he could already touch them. He was already keeping them immortal by his own power (and had been lying to them that he needed them to stay close "to avoid straining his power"). He could already reach at least to the edge of the solar system from earth if not farther, could already set theorems and forget about them. And AGAIN she tries to protest/question and he cuts her off, specifically with this being where he openly admits "there can be no forgiveness for me." And he says "even though" he rips the fingers from his hands but, considering the analogy he just made, well. It feels a lot more like that's one of the reasons why: because he's a coward who let so many of his friends die and has been willing to lose more and more to the RBs over time.
So yeah, jumping back up to the third screenshot up:
"I let them die because I thought that was easier" could be, like much he says, Technically True, just 'let the rest die because it was easier than explaining to A&M that he never wanted this and could have stopped it if he'd been paying closer attention, and hadn't lied to them in the first place about "needing to stay close to avoid straining his power".'
And back on Anastasia and Samael, I agree with asafeplaceforus112 on that. John's absolutely lying about "the secret was to do it slower—more methodically", because that very much was not his secret or how he did it at all. He was under far more duress than Mercy or Augustine, even! But lying in some regard doesn't mean he can't also be doing a lot of the Technical Truth or giving truth-adjacent details. And we DO know of a better version of Lyctorhood, one that you might even call true Perfect Lyctorhood if you trust Paul's judgment that "we are the love that has been perfected by death," which would, in fact, have killed them both. If they were about to figure out the Paul method, John's intervention very much would have technically saved Anastasia.
Maybe she really did panic halfway through, was an unsuccessful Orpheus not quite as fierce-willed as Camilla, who Pal urged whatever she do, just don't look back. Maybe John is the one who panicked halfway through upon realizing this was going to be Different (man who hates change here), realizing this would create a person he didn't know and thus wasn't sure he could trust, and/or fearing that learning there was any other way would make his other friends upset with him or lose faith in him. Maybe he panicked in a way that distracted her and made her panic before he actually jumped in. One way or another, I feel like that's what they actually nearly figured out. Team 69 parallels across time and generations.