I've noticed too and have been talking about this extensively with @domlerrys. I do think they're in the Book of Life, since everything is. But I think they did not disappear for, essentially, the same reason Crowley's imagination allowed him to pass through hellfire in s1. Let me explain what I mean by that.
The thing is that the GO universe is consistently shown to bend around Aziraphale and Crowley in slight but significant ways.
Those qualities that make the two of them unique* are shown to be so powerful and so meaningful as to fundamentally alter the fabric-stuff of the universe.
Hellfire is more powerful than demons, but Crowley is capable of weathering it by the extraordinary force of his imagination. Aziraphale and him are the original yin and yang of the universe, and birds sing when they are in balance. When they fall out -- truly fall out -- for the first time in over 6000 years, reality around them gets just that tiny bit harsher and more unforgiving, dealing fractionally worse fortune to the people caught in the area of damage, to the point of causing tangible effects. That's Whickber Street after they break up.
They unwittingly placed an engine at the moral-spiritual center of the universe and they keep it running by choosing each other again and again. Crowley giving up the Bentley to save the bookshop; Crowley later picking the bookshop as the last place on Earth in the whole of existence...
The GO universe runs on their love.
Think of it as a dying light, after the imagery we're shown in the movie; the core of the lightbulb would still be hot to the touch after it's been turned off, and would be the last thing to grow cold.
Hence why they "unexplainably" continue to exist after the Book's destruction, within the protective bounds of the only thing crowley saved, their home and symbolic keeper of their love.**
One of the core GO messages/ideas is that Aziraphale and Crowley's love (for the stars, music, food, books, plants, humanity... and, most importantly here, for each other) is the most powerful force in the universe, and having the universe show bias around them is the allegorical way this concept is expressed diegetically.
*As the beings who originated the act of defying one's prescribed role, crowley with desire for knowledge aka questioning God, aziraphale with desire for another angel aka putting something above the Great Plan.
**Unsurprisingly, in the movie this is also when the story turns explicitly meta-aware of itself, as the whole of reality has shrunk down to just around Crowley and Aziraphale and their continued existence calls the core diegetic rules of the GO universe into question.
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