Cannon Overview

The RNJR Cannon or the Shattered Dawn Cannon is a Fanon Version of the RWBY Story that retells the story using existing elements and Custom Elements without completely reinventing the wheel. preserving the General structure of the story but retelling it in a new and more Fleshed-out way that gives a spotlight to side characters and dramatically widens the scale of the story to many characters and stories.
The method of handling characters is inspired by Star Wars, giving otherwise nameless undetailed characters background for the purpose of giving everything going on in the main story much-needed context and opening avenues for telling new stories alongside the main. The world is meant to feel more authentic with a fleshed-out political background as well as much-needed rewrites centred around the Show's dialogue about Race and various other issues.
It fully expands all of the Kingdoms but none more so than Atlas, which gets a brand new Civil War storyline that feeds context for Atlas and their paranoia as well as the slow descent of Ironwood. The Cannon also rebalances story pacing and begins certain plot lines earlier, restores some scrapped concepts and sometimes outright rewrites entire concepts. The Story Structure is largely the same up until after Volume 3 when the timeline fully diverges into its own retelling of Volume Events and its own outcomes for those events.
It also writes Grimm very heavily giving much-needed details, classifications and a fleshed-out backstory of their slow descent into creatures of pure chaos and destruction, even for the natural world around them and not just humanity.
As such, all of these Rewrites affect the canonicity of various RWBY Campaigns, side stories and extra content not included in the Main Show.

Themes & Changes

Shattered Dawn pretty much attempts to do what any other overhaul Fanon attempts to do and that is fix what the Author sees as a problem in the story and tell a fun story at that. The Main Show started many years ago and much of what we know was created alongside the show. This has the experience of seeing the setting Grow as you get older but it leaves untapped potential in prior stories and character arcs that could've led to a richer story if certain parts of the lore existed earlier in the show.
Shattered Dawn is largely about set-up and delivery, many Complain about Ironwood's downfall even though his downfall is in theme with the show's subtle foreshadowing and themes and this is largely due to a disconnect between prior content with the current. Ironwood in Shattered Dawn is identified to be problematically authoritarian right fro the start but not inherently heartless or a bad man.

White Fang

This Fanon also completely overhauls the White Fang Storyline, rather than trying to erase what already existed, the Fanon continues with the idea that the White Fang is a Civil Rights Advocacy Group gone wrong. Rather than the main characters basically just being tools of the state wiping out terrorists. The White Fang is opposed by former members and many far more moderate Successor factions with this being shown right off the bat with the Egalitarian Society defending their human members from White Fang Attacks, the Egalitarian Society being a multiracial Civil Rights Activist Group.
This shows that the White Fang was once Noble and that Legacy continues even as the faction itself degenerates further into zealotry and bigotry. The Successor groups are a thinly disguised call back to actual Civil  Rights groups with platforms of Socialism, Decolonization, Egalitarianism and of course, Anti Racism. The Egalitarian Society is pretty much a Martin Lutheresq group but if their host country was with them and the leader wasn't assassinated.
The White Fang is a story of internalised racism turning Victims into the Very Oppressors they set out to oppose.

Geopolitics and Politics

During all the cool fights, flashy monologues and epic set pieces, politics is grinding away. every conflict you'll see in the Shattered Dawn Continuity is a Conflict that was long in the making before the main cast ever set foot onto the stage. This is because the Cast was a bunch of young people trying to find their way in a world that is much older and much more complex then they realise.
This idea was lost pretty early on with the focus being set on the characters and specifically a narrow set of characters. Shattered Dawn makes new room for this theme to persist even as the main characters go on about their Journey. Ruby Rose is on a journey to save the world, but is she a lawyer? No. Is she a national leader? No. Is she a councillor in a council? No. Ruby is a fighter and she is integral to salvaging this awful situation the world finds itself in but she and her party isn't the only piece of the puzzle.
As they go along their journey, there'll be signs of other characters far, far away from the main journey still doing their part. Whether it is the Egalitarian Society pressuring legal reform, or secretive Whitecliffe covert ops teams deep behind enemy lines taking out problematic figures before Team RWBY ever steps foot in a nearby land. If it is National Leaders securing new funds or General Ironwood directing his men to fight in a crucial operation against the Grimm.
The World is always moving and not everything is going to make sense from the perspective of one set of characters.

Atlas

I'll be hinting a lot about the changes to Atlas and its arc throughout this Document because Atlas is essentially the single most important Kingdom in the entire world, it is the sole superpower in most iterations of the RWBY story including the main one. As such it's the nation that deserves the most precision and build-up because what happens to it, deeply and adversely affects every single thing, event, and character in the entire setting.
In the Main, Show RWBY sets Atlas as the Protagonist and decides that the faction themes later on actually make it a more fitting antagonist. The Problem was the disconnect between Prior content and current. Instead in SHattered Dawn, Atlas fills a Moral Grey area and is an examination of Super Powers trying to be the sole Guardian and world police of everyone else and how centralised power always ends up being abused, whether malevolently with Jacque Schnee or benevolently with James Ironwood.
Rather than depending on monstrous acts to make Ironwood an Antagonist, the simple realities of his job and the war he's fighting are what eventually turn him into an opposing force against Team RWBY and it isn't a fighter either side wanted.
Early On, Atlas establishes itself as a force for the Greater Good, yes they are an expansionist Aggressive militaristic force basically occupying foreign nations that are their 'Allies' but without them, the Grimm would overwhelm the world. Atlas is always thinking in advance but it's thinking like anyone else is imperfect and influenced by many factors such as Fear, Hatred, Greed and Pride and Atlas suffers all of these.
ironwood is the figurehead of this struggle, his emotions tamper with his ability to lead and he makes crucial mistakes that set him and the Kingdom down a Dark path of War against its own sister Nation, Whitecliffe.

WTF is Whitecliffe

Whitecliffe is a Custom Republic, it is one of the few countries like Mantle or Menagerie that isn't a Kingdom and in Whiteclife's case, this is literally true as they have no hints of royalist past or culture. Whitecliffe is pretty much Volume 1 - 3's idea of Atlas being separated into a separate nation. Whitecliffe is actually Atlas but a rouge state within Solitas. Whitecliffe is an examination of how a country might do everything right and yet still end up in a terrible situation.
It is progressive, and democratic, workers get their fair share and are treated well. Faunus live happily free and equal lives with the City being a utopian beacon of Hope across the Globe. its army is small but efficient, deadly and well-studied against the Grimm. it has its own unrecognised Hunter's Academy and its only highly sophisticated technology and its own large global reach.
yet despite all of its power, being the only one capable of rivalling the City of Atlas, Whitecliffe is alone. RWBY is a story about how the world has to come together against all odds and work to beat a greater threat. In our world, this is Fascism, Environmental Crisis' and more but in RWBY's world there are similar hazards that most would name the Grimm. Whitecliffe alone cannot defeat the Grimm and Atlas Separate, and nationalists cannot unite the world against the Grimm.
It also serves as justification for Atlas' concern over a new Great War, Republic Whitecliffe and Kingdom of Atlas are completely opposed visions for what Atlas should be. Appeasement is failing over the years and war is looking more likely since the Fall of Beacon. Nations want to know which hside to bet for, many like  Whitecliffe, because it is benevolent if not militarily weaker in numbers and Atlas, is hated if not Militarily superior in numbers.
There are also many other factors that change and alter alliances as the story goes on. To make matters worse not everything about Whitecliffe is justified, despite years of successful progress it is still an aggressive militaristic State, with a hatred of all forms of Tyranny. It engages in a Cold War with Atlas and has responded nearly unjustifiably aggressively to many provocations both purposeful and Accidental. 
It has a murky past of getting involved in other country's matters it was never invited to and is a continuously aggressive agitator for rights even when it is not politically expedient to be so. Its Hyper aggression causes others to ignore its warnings of intelligent Grimm and of Humanoid Grimm and it has contributed a lot to Global  Tension around the world.

The Purpose of Mistral and Vacuo

In the main show these two Kingdoms functionally serve no purpose than to be background set pieces, details are scarce and even world-building on their cultures is surface level or scarce. This is likely because Mistral and Vacuo don't serve big important roles at the moment. In Volumes 4-5 we saw some details in Mistral and despite its Eastern themes, there is a lot of westernisation in Mistral, why? This is never answered .it's a subtle, compelling piece of world-building that is never touched upon. 
Vacuo is a broadly African / Middle Eastern-themed country with little to no detail at the time of writing (Context: Volume 9 isn't even out yet). There is a lot that can be done with Vacuo in the show yet until now, nothing has been done. Locations are almost like DLCs being released in a Game, places that virtually didn't exist until the authors introduce them for a set piece for a specific story.
As Such, Mistral and Vacuo in Shattered Dawn are stories of the Exploitation of Failing States, the Ravages of War, Climate Change and how an Empire falls. Mistral was once this vast empire that stretched all across Anima. It was the second greatest power to Mantle and both went to war against Vacuo and Vale. The Great War Video only goes into scarce video and while Qrow's narration is highly entertaining...it leaves a lot to the imagination.
In Shattered Dawn, Mistral's Downfall is continual, crippling treaties, bad loans, and terrible management and Imperial Rot has left this Kingdom bleeding territory to Grimm, Raiders, Atlas, the SDC and insurrections from within. Cities are rotting relics of an imperial age. This rot is a failure of reconstruction after the war leading Faunus hatred to rapidly spiral out of the country making the Kingdom's White Fang problem the worst in the world.
Vacuo is no better, the country isn't even real outside of the Walls of Vacuo City, most of it being barren desert Wastelands destroyed by unsustainable Dust extraction sapping the land of its life and worth. Despite winning the War, Vacuo was left with nothing but ruins and economic decline and a lack of aid. This turned Vacuo into a failed state with corruption running rampant, bloodthirsty warlords and ever more territory being eaten up by the White Fang who acts no better than the raiders they came here to defeat.
Grimm Devastate both Kingdoms as Desperation is a Great Attractor, leading to Atlas and Whitecliffe staging an endless list of interventions to save cities and Settlements from the Grimm and Raiders.  Vacuo hates being told what to do but the SDC's money is just too tasty for corrupt Vacuo officials to ignore, leaving Shade Academy as the sole beacon of Unity, Dignity and culture left in Vacuo only to be destroyed and actually forgotten about by the rest of the world.
Beacon's Fall set the world on fire, and Shade's fall was but a footnote in a Report.

The Schnee Dust Company

The SDC is introduced as a shady company that extorts the poor in wage slavery and contract abuse with the show lightly touching upon these themes. We're told the SDC is bad yet all of their depictions portray them as weak victims with even Jacque Schnee being a wet noodle who can barely hurt fly even if he really tried to. While hilarious, I see this as a mistake. As such, I gave the SDC a massive villainous glow-up.
Complete with War Crime-Ridden Private Military Companies. Completely unethical business monopolies. Stupid control over currency and highly toxic, Corporate conservative views on Corporatism. Jacque Schnee is re-cast as an independent Villain separate from Salem and Adam completely. Jacque is on his side and no one else's. All he cares about is the family legacy and dominance over all things. 
He is still abusive and it's still petty, spiteful and pathetic but there is a malevolent controlling edge to it. The SDC pretty much control Atlas and through Atlas controls the world by controlling all of the Dust extraction and Refining, even doing it to extent that it turns entire provinces into unlivable Desert Wastelands like Vacuo or the Wutan province in Mistral. Jacque will do anything and kill anyone or anything to win, because that's all that matters to him, Winning.
Slavery is no longer lightly implied but outright committed by the Company, thinly disguising it as "Special Employeement' with contracts and they are allowed to do this because who's going to say no to the guy who owns all of the energy production in your country? The person dying of cold in winter, that's who.  or worse, dying to the Grimm because your defences can't be powered.
The SDC is pretty much a lot like Shinra from FF7 but unlike Shinra, it cannot be redeemed. This is because giant Mega companies are beholden to no one except themselves and this is shown throughout the story in many forms. 
This much more Evil Version of the SDC is what contrasts against Weiss Schnee, and sells her story of being reformed. In Shattered Dawn, Weiss is actually loyal to an antagonistic Faction but by the end of Volume 3, has completely abandoned it because she knows the truth. The SDC being like this also serves as a reason why the White Fang turned so insane and why Adam was damaged in the way he was. he was born into slavery and branded like cattle. Dooming him to a life of hatred and spite. 
This plays into Blake's Storyline and helps her character draw a line between walking away from the White Fang and Siding with the State and its corporate allies/ overlords because she hasn't.

Unfucking the Ages

I gave 2 years between Vol 3 and Vol 4 for 2 reasons, one was to give time for events to happen and things to space out for believable developments and I refuse to have a 16-year-old Protagonist and then have a ship with 14 year old in a cast of much older characters. Instead Ruby by Vol 4 is 18 and Oscar is 16 and they have a Brother - Sister dynamic instead. Seriously this ship makes me uncomfortable.

Grimm & Salem

The Grimm and Salem decided on a very dark theme for them, not only is the land they dwell on a Named fallen Kingdom, Astroa full of ruins. They also have sick and twisted designs and a hidden Master who is pulling the strings of the world for power. The Grimm are a dangerous, Viral Plague that is designed from birth to Kill, devour and destroy everything in its path with absolute wanton disregard for all life all Grimm not having these traits being killed and (Rarely) being domesticated by others after saving them from the Grimm.
The Grimm are monsters but they also have Humanoid variants that are intelligent and increasingly more common after Volume 3, they are an ever-evolving threat to all life on the planet. They were not always this way and a long string of events, corruption and mutation made them this way. They are the creatures of Darkness and if they ever finish with Remnant, will move on to devour every world of all life until the last star goes out.
They are not just scary, they are bloodthirsty, cruel, disgusting and creepy. They use everything against you, even your own friends and family. Nothing is below a Grimm, they are creatures of engineered Pure Malice and it shows in their sadistic torment of everything they find. This Cruel and corrupt nature is replicated in Salem, who preaches higher lofty goals but she is no different from the beasts who serve her.
Only wanting Power, having long forgotten why she was even fighting in the first place, just like the Grimm. A World of Bloody Evolution, that is what they desire.

Whats Cannon

The Main Series is closely mirrored by the first 3 Books of the Shattered Dawn Continuity, though similar events happen the exact methods of getting there can be different. Character relationships are largely what's most divergent in Shatter Dawn's first 3 Volumes compared to the main series. Shattered Dawn also references a lot of external events and does a lot more world-building than the main series.
Expanding on concepts, however, if you were to forget shattered Dawn's events and instead remember only the Main series' version of the story, you'll be more or less correct about what actually happened. After Volume 3, the continuity goes down a similar Journey but told through different perspectives. RNJR Isolation covers Weiss' Blake's and Yang's version of their Volume 4 journey while RNJR: Serpent's Crossing covers the events between Vol 3's ending and the Vol 4 teaser when Ruby defeats the Grimm in the village, now named Serpents Crossing.
The Further in the Main Series you go the less likely it is canon in Shattered Dawn, with the story completely departing from the main series in the Atlas Arc to pursue a different story trajectory compared to the original.
Another thing to note is that in Shattered Dawn, the Character flaws of the main cast are highlighted in more potent ways. Yang has Anger issues, and Weiss is recovering from Programmed racism. Blake is a survivor of abuse and Ruby is in over her head. Lots of side characters get more spotlight as well with massive changes happening for Cinder's Storyline pursuing a Scheming, and Cunning Villian Archetype who is on the path of Redemption but still makes a lot of mistakes and missteps, inspired by the Storyline of Zuko from Avatar which her character design references so thoroughly.
Salem also gets a new Storyline with her rewrites affecting most of her underlings, she is rebalanced to be a much clear threat to the Globe.  She is now much more obviously the big Villian of the Story with her villainy being added to from the revoked villainy in Cinder's storyline to preserve narrative Balance.

Grimm Eclipse is the 2nd most Cannon entry into the Rwbyverse as far as Shattered Dawn is concerned, Eclipse will get its own side novel with the Main characters being Ruby Rose, Blake Belladonna, Jaune Arc, Pyrrha Nikos and Cinder Fall with the side cast being Emerald Sustri, Mercury Blake, and Professor Oobleck who is overseeing the mission. Dr Merlot is canon as are his experiments.
His story will be an optional piece of content that hints at the Darker Side of Atlas in more potent ways early on in the story. 
The Story still takes place at the same time as the Game Takes place, Between Volumes 2 & 3.

Elements of the Grimm Campaign exist, such as the very Location of Kuchinashi itself, however, that's pretty much where it ends as I do not know the full story of the Grimm Campaign, rather Kuchinashi is a set piece that'll be revised many times existing as a microcosm of the Collapse of Mistral and its eventual restoration throughout the events of the books and various side stories.

Due to changes in the Main story and Nolan Porifiro being added to the main cast during Volume 4 as well as Cardin Winchester's entire fate being alternate. The After the Fall Novel is considered utterly non-cannon but will get a side story named Aftermath that covers the perspective of all the same characters and their various missions across Remnant covering off-screen events such as the Collapse of Vacuo and the Fall of Shade Academy.
It will also include events going on in Mistral outside of the perspective of the Main Caste, the Main Character will be Caffeine herself as she does her best to salvage a Bad situation going to worse. Aftermath will also show exactly how the world is responding to the events of Beacon and provide even more context for the Country's behaviour throughout the Volumes.

Arrowfell is too late in the Rwby Timeline to be to Cannon as the Atlas Arc is completely rewritten but the characters in it may get put into Shattered Dawn's Atlas Arc and bring much-needed padding and lore to Atlas itself. 

Ice Queendom was released after Shattered Dawn's first 3 Volumes had been written and despite Ice Queendom being my personal favourite of all the side content of Rwby, it is not considered Cannon, not Shattered Dawn. However many elements of its story are translated into Shattered dawn with Shion Zaiden existing as is the Nightmare Grimm she hunts. Rather than just being the Nightmare Grimm an entirely new Class of Grimm exists that fills similar purposes.
The Actual Nightmare Grimm we see in Queendom is fully evolved by Volume 4 and is used on Cinder to try and control her, it is also revealed that Cinder had an earlier variant of the Grimm infecting her since she joined Salem, making her more sociopathic. The Nightmare Grimm is planned to be used more in the Atlas Arc for character development surrounding Penny Polendina, Cinder Fall, Adam Taurus and a few others.
it also is used as a way of showing how the Grim mare evolved to use Humans against other Humans. The Apathy Grimm is also a part of this theme.

Because I have yet to Write Aftermath which is Shattered Dawn's version of After the fall, I am unaware of how much of this book can be applied to Shattered Dawn's Cannon and is thus currently non-cannon and may not get a Shattered Dawn version of its own depending on how Aftermath Develops.

Despite the Details of Roman Torchwick being a bit different, Neo's Inability to speak is caused by voice box removal in a bout of gang violence at an early age. This Book should more or less still be coherent with Shattered Dawn.

I am largely unaware of what happens in these sets of Legends but they should more or less still be applicable to Shattered Dawn and if not, well not all legends are accurate.