The Books of Sorrow describe the Hive destorying the Ammonites, a race of cephalods. The Traveler also created several Golden Ages before leaving them, why would it destroy everything its built by its own vanishing act?
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Well, according to those same posts, it specifically left the fallen because they were doing terrible things that it didn't want to be associated with (which I wouldn't mind an elaboration on). The only answer to your question that's not weird is if it did that on purpose/didn't care if it made that happen.