Welcome to the Lynxverse!
These are the most important differencs between "Star Trek canon" and the Lynxverse.
1. The disgusting and patheitic creature which showed up in a horrible season 6 episode of Voyager wasn't the real Kes but Suspiriia in disguise or maybe a being from an alternate or mirror universe.
The real Kes was restored back to normal from becoming an energy being ( VOY episode The Gift) by Q. She got a human lifespan but had some of her Ocampa mental abilities which she showed up in some episodes intact. While searching for Voyager, she encountered a Maquis ship which had been taken to the Delta Quadrant by The Caretaker. After a brief encounter with Voyager which included some adventures, she followed the Maquis ship to the Alpha Quadrant and now lives happily on a planet together with some former Maquis and other colonists. The planet is located somewhere between Bajor and the Tzenkheti Alliance. Her will to explore and discover sometimes leads to exciting and even dangerous adventures.
2. The "Gowron" who was killed by Worf in the DS9 episode Dogs Of War wasn't the real Gowron but a genetically altered Cardassian agent who during Cardassia's collaboration with The Dominion had been sent to Quo'nos in order to destroy the alliance between the Klingons and the Federation. The real Gowron had been kidnapped by Cardassian agents and taket to Cardassia.
When The Dominion did surrender, Gowron was set free from a prison camp on one of the worlds in the Cardassian Union and sent home to Quo'nos where he got his place as Klingon Chancellor back. Martok remained the Supreme Commander of the Klingon Forces.
3. In the novel Second Self, The character Garak is destroyed as a character and killed off.
We have also had movies and series where the planets Vulcan and Romulus had been destroyed.
And the Klingons have been turned into something which looks like Mutant Ninja Turtles
But all of that happened in an alternate universe called Dystopian Hell Universe of 2000 where all episodes and books containing events in NuTrek movies, Star Trek Discovery and Star Trek Picard takes place.
In the real Star Trek Universe, Vulcan and Romulus still exists, Garak is alive and well and there are no Mutant Ninja Turtles "Klingons" to be seen.
The events in the Voyager episode Threshold never happened. It was just a nightmare Tom Paris had after eating too much of Neelix's food.
Captain Kirk never died in the Nexus (The movie Star Trek Generations). Those events happened in an alternate timeline.
Those are the most important differences between "Official Star trek canon" and the Lynxverse.
There are more which can be discussed later and more will occur as the Lynxverse expands.
