Scott Snyder talks about the history kept and lost (among his rise to being the lead writer of Batman) in his chat with Kevin Smith's FatmanonBatman podcast series here: http://smodcast.com/episodes/scott-snyder-of-cowls-and-owls/
To paraphrase the segment: writers were given the choice to establish what was canon and what wasn't--and because Scott and the other writers in the Batverse were so connected with the previous history all of the main events [such as Cataclysm, No Man's Land, Knightfall, Hush] remain intact, though they may not be referenced towards they won't try to refute said events.
He also mentions how writers of other Batbooks start unweaving mythos (like Teen Titans with Tim and RHatO with Jason) but the guidelines the Batfamily, at least, is going off is entirely pre-New 52.
I wish each major writer were able to have sit down talks like this. Knowing if Supes has died at one point is sort of important in how Superboy comes into being. They wouldn't even need specifics, just hint at "yup he died against ___ and that event's overall impact did still happen"
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