It was only in Holdstock’s TDW novella where Raxxla is already inhabited by corrupt twisted men. It’s possible that is carried through, but I suspect more likely that was also retconned with the rest of the book.
Has anyone got a list of lore & links to the source FD statements about what was retconned?
TDW hasn't been true lore since FE:2 was launched. ED lore has it's roots in the Gazetteer that came with FE:2.
http://www.dream-ware.co.uk/frontier/books/gazetteer/
From what I have seen most of the events from FE:2 and FFE(up to the branching point of the Thargoid story), has been kept as it was.
Notable exceptions from this is the extensive cloning in the Empire and the large sentient android population of the Fedration. These seem to have never existed.
Officially the lore of ED are the sanctioned books and anything in the game(Galnet, beacons, mission texts and so on).
The so called retconn that happened, has never been fully explained. From what I have understood it was change in direction compared to what the writers were told, regarding the contact between the Alliance and the Thargoids in the 3250s. It was far less dramatic than some anticipated and only a few details in 'Out of the Darknes' was affected.
The explanations FD have given regarding The Dark Wheel, is that it's not to be considered to reflect actual events that happened. It's to be considered as a legend within the game. It like the book exists in the ED galaxy, but it's not a historically correct text.
It's probably like watching Braveheart or Gladiator on TV. Mostly entertainment, but with a few historical elements.
As we know from the Codex, it's not out of the question for an author in ED to have concealed secret information in a book.
In large i don't think the retconn is anything to worry about, when it comes to Raxxla. There was neve anything to retconn. Official lore about Raxxla is only the codex (none of the mission texts actually mention Raxxla, by name). The Codex hints that clues may be found in works of fiction. This means that valuable information may be found in non lore writings. The Dark Weel is probably our best candidate.