It is unknown whether the published novel is the same as the version in the typed manuscript on Flight 815. There may have been multiple manuscripts, or the publisher published an earlier draft submitted by Gary Troup.
Based on appearances, the manuscript appears to be a screenplay adaptation of Bad Twin, perhaps written on spec by Gary Troup. He may have been flying to Los Angeles to take Industry "meetings" about his Bad Twin screenplay.
The novel references the detective novel Trent's Last Case, which it describes as being solved halfway through, but then is proven wrong and has to be resolved. It could indicate that the reasoning presented at the end of Bad Twin to explain events could be wrong. With the fuss the Hanso Foundation makes about it, they could be behind the killings therein.
Chapter 10 has a part where Moth, a friend of Zander's, once thought that Zander "looked like a goddamn clone of Cliff," possibly referencing one theory that exists on the island.
The book jacket notes that "Bad Twin" touches on the themes of "good vs. evil, purgatory, and redemption," further confirming these themes within the "Lost" series.
Purgatory is referenced outwardly numerous times in the book.
First mention is Chapter 14, when Paul Artisan is going to meet with the coroner: "The doors finally opened on a spotless, glaring hallway, a sort of pit stop on the way to eternity, a purgatory of bright white tile and fluorescent lights."
Later, in Chapter 15, Manny Weissman and Paul Artisan discuss the concept of purgatory at length: "Fascinating subject, purgatory...You've read your Dante, I hope?...The Paradiso is a total snooze. I mean, eternal bliss is probably a nice thing to experience but as a subject for poetry, it stinks... As for the Inferno, it's got some great gruesome bits in it, but it's mainly Dante coming up with sadistic torments... But the Purgatorio - that's an amazing and exciting piece of work....That's where everything is up for grabs. The stakes could not be higher. There's suffering, but unlike on earth, the suffering isn't senseless and random. It has a meaning and purpose. Destinies balance on a knife edge. The slightest slip dooms you to perdition. Not just for a while. Forever. No more second chances - Purgatory is the second chance, the last chance. The hard road and the only road that can lead on to redemption." - Troup, Bad Twin, p. 99
Manny's dissertation to Paul is referenced in Chapter 16: "What Manny Weissman had said about purgatory was also true of cases in which people died: Destinies were balanced on a knife edge; between life and death there was little room for error or time to recover from a stumble, and for some people, at least, there would be no more second chances." Troup, Bad Twin, p. 106
Jack, in "Tabula Rasa", says to Kate, "What you did before the plane crash, what you did then, it doesn't matter. Three days ago, we all died. We all deserve a second chance." Interesting...
The book also references being in "another world" many times in the novel, especially in Chapter 14: "His hands were clammy, and as if by instinct, his eyes sought out a window, an escape, an assurance that there was still a world beyond this glaring antiseptic chamber." (p. 87) A couple pages later, "When [the door] closed again, there was a slight whooshing sound, as if the worlds on either side of the door had different pressures, different atmospheres." - Troup, Bad Twin, p. 89
In Chapter 16: "Maybe death was even more more unsettling on an island. Maybe it seemed like an obscene visitor from the world beyond, an uncouth guest that carried not just a single tragedy but the threat of some horrible contagion."
This references not only the "other world", but also the concept of The Island and something like the sickness.
There are at least two instances of glaringly bad word usage, perhaps intentional? Example, page 207 "Not too sure I feature that" - "feature" being used in a sense of "would like".
There are also examples of strange observations through out the book, such as on pg. 33 Artisan notices Cliff Widmore's lavender shirt but on pg. 45, within the same scene, he comments the shirt is mint green. Now these instances could just be sloppy editing but also could be a comment on perception. The Lost producers' attention to detail is extraordinary so could the instances of bad word usage, which is referenced in the previous bullet point, and these observations be something that just slipped through the cracks? Maybe not.
There is a reference to an ancient map on the wall in Widmore's Locust Valley estate of Caledonia, which is one of the old names for Scotland, BUT New Caledonia is also currently an island off the eastern coast of Australia. There may be a connection.