FoA and the Macgregor novels are still canon (says the Lost Journal)
I went out to Barnes and Noble tonight, and found they'd put out the Lost Journal of Indiana Jones book a few days early. So I snapped it up. Intriguingly, there are almost zero references to non-filmed Indy stories: YIJ and the four films take up most of the book. Understandable, as many such sources are extremely dubious story-wise.
However, there are a few pages of the journal devoted to Fate of Atlantis and Indy's relationship with Sophia, plus brief references to the Seven Veils novel and Deirdre Campbell.
So apparently Fate of Atlantis (and Rob Macgregor's novels) are good enough for the Lost Journal writers to include mention of them with the filmed Indy, but nothing else? Well, if we have FOA at least...