Booker's who accepted the baptism were drowned. Therefore Comstock ceases to exist. But Booker who did not accept baptism won't be drowned. If you watch until the end of the credits, you see Booker walking into a room with Anna in the still in the crib. Therefore Booker still exists, Comstock does not, the Luteces never give him Anna, and Columbia never exists. But since Columbia never fails, Andrew Ryan still builds Rapture.
Also: foreshadowing, when you get baptised to get into Colombia, Booker says: "that preist needs to learn the difference between baptising a man and drowning one"
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