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So, to start with, I should probably point out that Deconstruction, as it's used on this wiki, refers to when a trope or genre is played very straight to show its illogical or unrealistic nature. It's often confused for Dark Fic, as the line between "realistic" and "edgy" can be kind of hazy sometimes. The main questions to ask are "Is this based on something in the canon work, or is the author taking some creative liberties to seem darker?" and "Does this seem more realistic, or is it just being dark for its own sake?" See Not a Deconstruction for more info.
- Kazuto at level 90: I have no idea who Kazuto is, why he needs to outlevel the other players, or how the others can "take time out of their real-life matters to level grind"; I thought the whole premise of SAO is that the players were trapped in VR. So it's lacking some important context and I can't analyze it.
- Ryotaro and Grandis: First off, are those two the same person or something? The example doesn't say anything about it, and I've never watched this anime, so I don't know what the connection here is. But anyway, this isn't a deconstruction, it's just a one-off snarky quip.
- Code Lyoko and Ascended Fridge Horror: As you said, the example outright admits that it wants to be AFH instead. Except that fanfics can only ascend fridge horror from other parts of the same fanfic series. Cerebus Retcon is a more applicable trope here, as that trope has a lot of examples of "fanfic reveals the dark origin behind a not-particularly-dark canon thing".
- Harvesting legendary Pokémon: This is a perfect example of what I said earlier about taking creative liberties to be darker. Nowhere in Pokémon canon does it state that legendaries can be harvested like that, nor is it stated that anyone is interested in making armor out of Pokémon parts.
- Lady Sigma: What exactly is being deconstructed here? I have no idea what kind of antagonist Lady Sigma is, and averting a trope is Not a Deconstruction of it. I guess I could maybe see how it's a deconstruction of something like Ax-Crazy if that's applicable to her, but there just isn't enough info here.
By the way, you should take questions like this to the Is this an example?
thread next time.

https://tvtropes.org/pmwiki/pmwiki.php/DeconstructionFic/CitadelOfTheHeart
So I have been reading this page, and I am not sure that some of the examples really come off as Deconstructions
For example:
"Sword Art Online: Special Edition's Kazuto is a slacker who appreciates reality more than gaming, and believes staying at the Level 90 status he was in the actual game wouldn't be anything he'd have to worry about soon. Then shit begins to hit the fan and he and the others being to hastily take time out of their real life matters to level grind to deal with the associated threats at hands. Considering Kazuto was already rather high in level by MMO standards, he's shown later to not be far off from the (initial) cap in how high he had progressed so shortly."
These examples do not explain to me how something is being deconstructed (and honestly, in my opinion, do not come off that way, especially the second example)
"Some of the stuff from Code Lyoko becomes Ascended Fridge Horror because some of the nightmarish qualities of the show are given completed context. Project Carthage? An Ultimate Lifeform in the form of Mirror M that was created to be used against the Nazis in WWII. The Digital Sea? A weapon gone horribly to try and eliminate Mirror M twice. The fact that death cannot be reversed by the Return to the Past? Even Mirror M doesn't know that one considering he flat out admits he has no idea who the people even were that he was told he killed because he flat out can't remember they even existed..."
As even this example states, this does not seem to be Deconstruction but rather Ascended Fridge Horror. Or at least Cerberus Retcon
"Solgaleo and Lunala frequently have their armored bodies clipped and regenerated as to farm valuable materials necessary to craft armor that is designed to withstand the extreme environments of the Ultimorian Multiverse, since even the Ultimorian Deities themselves have major issues surviving there anymore. Grandis flat out admits that had Solgaleo and Lunala never existed nobody would've been able to go through there or into that place ever again."
This... feels nothing like what Deconstruction is supposed to be
And this... well... it also does not feel like the trope.
Admittedly, though, from what I have heard, there seems to be a lot of debate on what exactly counts as a Deconstruction Fic. But I feel like this page could be given a look on if all the examples it holds at least fits what is the basic idea of Deconstruction Fic