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I let it sync by itself if the WiFi is on. If I am concerned about the battery I turn the wifi off and then it doesn't sync. I sync manually if I have pocket articles waiting or if I bought new books. I have never had major issues with firmware (except maybe the dictionary lookup issue back in 2.5 I think it was) so generally I'm fine with upgrading, especially since I do prefer my books to be kepubs (so the notes sync if I make any).
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