https://www.tumblr.com/confession-of-the-heart-fm/824429152604225536/yeah-okay-can-we-talk-about-the-upside-down
Ooh, I know this one! Buckle up, this gets a bit long.
As with plenty of other things, the answer to “what’s up with Axel’s tear marks, anyway?” got a bit lost in translation. It’s made much more explicit exactly what the upside-down tears are, and where they came from, in the Japanese script of KH3. In English, the line Saïx gives Lea is “Always told you they’d stop you from crying, those upside-down tears”. In Japanese, it’s spelled out a lot more directly: Saïx says to Axel that he “taught your crybaby self that spell which stops you from crying—those upside-down tear marks”.
(Yes, he does just flat-out call Lea a “crybaby” in Japanese. It’s cute. If it weren’t for KH being E10+, I’d have said it’s more like Saïx says that he “taught your crybaby ass that spell” because that’s really more of the energy he says it with.)
Before anyone jumps to saying the English version is mistranslated, I wouldn’t go that far—I get the sense that the English dialogue was written to sound more like a natural conversation between old friends and less like exposition for the audience, so it relies more on inference between the characters on information they would both already know. Its meaning still largely captures the same idea in English, it just leaves out the nuance that Saïx is the one who “taught” the marks to him.
Anyhow, when Saïx says it’s a “spell”, in Japanese, I want to be very clear that what he means is the upside-down tear marks were a type of magic protection cast on Axel—the same type of “lucky charm” that is cast when two people feed one another paopu fruit. The reason this is so clear is because the Japanese word Saïx uses to describe the tears has no other nuance than “spell, charm, enchantment”, etc. The way the paopu fruit sharing and the tear marks are referred to in Japanese is unique among the “lucky charms” of the series, as they are the only two things that are referred to as “magic spells” (as opposed to simply being items that you carry around with you for luck).
Since Saïx attributes it to himself, the spell was likely either directly cast upon Lea/Axel by Isa/Saïx, or he taught him how to cast it upon himself. And, because we know from this remark the marks are a spell that had to have been cast by a specific person, this means that it’s highly unlikely they simply appeared on Axel’s face when he became a Nobody.
So if it was a spell, what did it actually do? Well, it did exactly what Saïx says it did: it “stops you from crying”. The Character Files book supports this, as it reiterates multiple times that the reason Lea is so sensitive and tearful all the time post-recompletion is because the marks are gone:
Lately, I’d been just a bit of a crybaby. Could it be because the upside-down tears had disappeared from my face?”
“You used to be a crybaby. Before I knew it, the marks under your eyes that stopped you from crying disappeared, and you began to make friends other than me and laughed with them.”
“In the end, you’re still a crybaby, but you don’t need those upside-down tear marks anymore. Just like you don’t need me anymore.”
This suggests that the magical function of the upside-down tear marks was to make Axel unable to cry.
Because of this, we can infer the reason the tears vanished when he recompleted as a human is that at the end of his life, Axel finally did cry. (During the scene where he says goodbye to Roxas.) This was a sign that the tears were no longer needed to protect him, and thus the spell was broken. That’s why Saïx makes that comment teasing Lea about looking like he needs the tears again when he seems sad, and how Lea himself talks about the tears as though he’s “outgrown” them and doesn’t need them anymore. (You can make your own guesses as to why a spell that prevents crying was something Lea/Axel needed in the past to protect him in the first place.)
The scene in DDD where Lea wakes up in the lab can be somewhat misleading for this reason. He concluded he was human again because he connected the dots and realized that the spell was broken as a consequence of his return to humanity. So, although their vanishing was symbolic of that—of his emotions finally returning to him in full—it’s actually not the case that the tears were necessarily some kind of physical mark he gained upon becoming a Nobody. They have a separate origin!
All this to say: Axel’s tears vanishing actually don’t suggest that physical markings (such as scars) gained as a Nobody vanish when they recomplete! The tears are their own thing. Go crazy with your Nobody scar headcanons, canon supports it! Saïx for example could easily have been scarred after he lost his heart, and retains the scar after recompleting either way.
I think it’s probable that these things will be spelled out further whenever the next entries expand on Lea and Isa’s backstory, since Nomura has indicated before that he intends to go into that at some point.
-- Saïx’s defense attorney (currently working other cases)