I just saw a video explaining/speculating how assassin’s creed origins and odyssey break assassin’s creed lore, but my opinion, my speculation is that it doesn’t break lore, it enhances it. I will explain.
When Desmond was in the animus, he wasn’t a researcher, he was an innocent bystander whoms memories were of great interest at Abstergo Industries. He didn’t have any reason to research his memories or any interest in doing so and he was forced to go into the animus, as he couldn’t leave the research facility, he was basically forced to be in the animus and only a puppet to his previous incarnations. He was being read like a book, nothing more. Off course, they can only go so far in this kind of animus, and research to different anima (plural of animus?) is constantly done, I suppose, so how farther we go into the assassin’s creed series, the more research Abstergo has done to improve their machine, as you can see in our own society, things improve constantly.
In comes Layla, the researcher that willingly goes into the animus she has, and willingly researches her ancestry and what they have done in the Assassin’s order. She willingly wants to know what has happened, and this is where the distinction lies. Desmond didn’t want to know, he was forced in the animus. He didn’t want to explore his past or what his ancestors were. He was forced, first by Abstergo and then coerced by the mercinary group from the second installment in the series.
You can see it as a puzzle piece. Desmond doesn’t have the complete puzzle and has no interest whatsoever in ever solving it. What they have is an incomplete puzzle that they have to make do with. They can look and research the puzzle, like with the Zodiac Killer puzzles. They weren’t meant to be solved, so it is damn difficult to do so, same goes with the Enigma puzzle, but eventually that one was cracked.
Back to Layla. She wants to solve the puzzle that is her ancestry, so she has control over her animus in a simulated enviroment to create combinations that might fit her ancestry DNA to decode it, much like a brute-force password cracker tries countless combinations to try and crack your password. Much like a puzzle that is unsolved, but for which you have the pieces, like a memory you can’t remember but it still lingers, you can feel it lingering. This is why her Animus is different, it isn’t a reading device, like the Animus Desmond had, but it works with Layla, because she is willing to research her past. Her Animus is a simulation that creates possible memories, that helps her explore the area of her ancestors in the hopes of making something fit her DNA. It doesn’t decode her DNA completely but it helps her create a possible scenario that might have happened in the hopes of decoding her real DNA and what happened there.