Halsey learns that sgt johnson was a spartan even though in first strike she apparently doesnt remember him she says borens syndrome was the reason he was immune to the flood instead of his Orion augmentations.While lore like that might not feel like a big break in canon to most, it is to me and A few others because it wasnt necessary.You didnt even need Johnson in this book.
Now, I'm writing this not having read Silent Storm yet, so if I need correcting, please do so.
Halsey read off Johnson's medical records to John in First Strike (pg 294-296). The records were made 3 years prior, as if he had just contracted the disease (on Paris IV), not as if he had the disease for some time (so by extension, his altered DNA shouldn't have been public knowledge). She could still have known he was a Spartan-I and only been given the medical records from ONI, who would, in their best interest, only divulge falsified information. Halsey doesn't know his actual medical records from his Spartan-I days.