The authorised novels were checked for compatibility with the lore by Frontier. So they won't contradict it - though, equally, most of them being written before the game released have some differences with the game itself: e.g. Reclamation refers to Imperial Couriers on the assumption that they're about the size of their FE2 namesakes, rather than light fighter/multirole ships (I believe later printings say "Clipper" or "Cutter" instead at that point); some star system names or positions don't quite make sense; etc. A lot of them, of course, don't really touch on "big lore" issues anyway; the tales of some space pilot in some miscellaneous system can be a good read without it mattering in the slightest whether it actually happened or is some tall tale told in a bar. (All of the stories from FE2's "Stories of Life on the Frontier" book fit into this scope, for example, and may as well still be "canon" today for all the difference it makes)
Equally, they're entirely optional. If anything is in them lore-wise which is necessary for players to know, then it'll come up in in-game sources too. So e.g. the Club being secretly behind some events (especially around trying to kill Halsey) was never mentioned in-game and only vaguely hinted at years later after Jupiter Rochester took the fall for it. But, equally, the various storylines work perfectly well if you don't know about them.
There's also always the distinction to be made between "X" and "Y said X". So we "know" about the Klaxians and Oresrians because characters in the authorised fiction have mentioned them. But that doesn't mean those characters were entirely correct - they may have been lying for their own ends, or they may have been misinformed themselves as part of some other plot. Some of the Azimuth logs hint that the current Thargoids aren't the same group as from the first Thargoid War ... but what that means, and how it fits in with the Klaxian/Oresrian split remains unclear.
The combination of those three means that there's quite a lot of scope for Frontier to have things referred to in the books have a different meaning to the obvious one, or perhaps even to the one that the author of the book intended, while still not outright contradicting anything. So, for example, the Club in Premonition is talked up as the uber-conspiracy: they're behind everything and anything, every single news article, CG, other event, etc. that took place in-game was in some way part of the Club's plan. More recent stories suggest that's not true - they're an important and influential secret group, but far from the only one trying to manipulate more public politics and events.
But that's not automatically a contradiction or a "retcon" - once discovered at all, there are advantages to a conspiracy being believed to be bigger than it really is, and its members are obviously not the most trustworthy people so anything they say about themselves might just be a lie (while Salome, of course, couldn't give a clear answer if when her life depended on it, and had an ego better suited to fighting "the conspiracy" rather than "a conspiracy").
With the story being pushed out in weekly installments, and limited at times by the need for the developers to catch up to the writers in providing in-game content, they'd be joining a long tradition of serial fiction writers who've decided a few years in to the writing that some early foreshadowing was actually for B rather than A - and no-one other than a few NDA'd authors who saw the original "A plan" need to know or care.
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