I honestly have no idea why the Lore Team felt the need to change material from the original, most of the time by deliberately changing what was in the manuals or Sonic Channel Posts, or just ignoring the past content in general.
A lot of the material they often seem to ignore, like the past confrontations between Sonic and Eggman or the nature of the Special Stages, seems to go with the idea of "It was only something from the Japanese material that was never used in English, so we need a brand-new explanation that can take from the original Japanese one and finally be used in English", when I think that just picking the original material and releasing again translated would have been enough.
Gerald's Journal is the biggest example to me of how confusing the approach to lore the Lore Team is. In part, it's full of callbacks to very small things and ideas that were only in the Japanese material, but then you have these odd things like leaving Gerald's mistranslated line of "making Shadow's mind perfect" instead of the original "I have perfect control over Shadow's memories". And this was also just in the English material; the Japanese version kept the original content with no changes. Why? From what Ian told, it was Chris' idea to reference the Sonic Channel story in which Shadow gets named by Maria and the others just didn't know a thing about it, so I think there's a lot of "We don't know what is in the website", which I think it's a mistake, they should have access and study this resource instead of writing without knowing it, if it reaches a point in which they all depend on Chris to make references to it, that can go wrong very quickly to depend on a single person.
At least from what I would expect, the solution to old lore being Japanese-only material that was never translated shouldn't be "let's make new lore and ignore the old one", it should be "Let's finally translate this untranslated material and have the whole world know it".
Although, I feel that some changes (Like Silver time travel being changed from Chaos Control to random portals or Blaze Sol Emeralds' not mentioning time travel anymore) are choices of deliberately changing something. They don't want Silver or Blaze to have control over their time and dimensional travel, as made clear not only from Bumblekast's answers back in the day, but also IDW that directly had then calling out their lack of control to explain why they can't just "fix things". And I personally dislike it, I feel like the answer to this is fully embracing what existed and creating something to complement the original material instead of ignoring or changing it to favor a storyline.
Honestly, I'm a bit surprised that Amy's Tarot Cards got back, considering all the other sides that were ignored or changed. Maybe it was different because at least with it they could create an easy-to-sell asset. Maybe if Silver's time travel was connected to some easy-to-make merchandise, they wouldn't have felt the need to change it.