I just got this update on my Aura HD and was bummed to see it messed up my collections. I only had two, but they were useful for the way I like to do things and one disappeared while three ancient ones long deleted reappeared and needed to be deleted again. Only the most recently created one stayed intact (although I'm unsure if it's missing any books or not). My collections are created and managed manually on the device.
Like I say I was bummed, but given that it's the first real issue I've had in three years I'm not too put out by it.
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