They're definitely *not* going to retcon all of Books 1&2. However, the events after the (veery weirdly edited) "encounter" of Zoe with the Dreamachine could be suspect to a degree. I still don't think they're going to tell us that they didn't happen, but definitely something strange is going on there, the scene transitions are very bizarre, very dreamlike.
^ This. I'm not sure what blowing up a handful of guards at the entrance to the Metro would actually accomplish, unless it was part of some larger plot? Or not actually real but a dreaming vision of what MIGHT happen, or a symbolic message to Zoe's dreaming mind, or.. or..
I'm keeping an open mind at this point about what did or did not actually happen. I think until I get more information I'll just have to place myself in the hands of the developers and let them wring all of the feels out of me until they're done.