Thanks a lot, guys! I've tried scanning the Kindle folder itself (not sure if that did the trick, "Repair" and such), and for some weird reason, I've tried using Calibre again, and lo and behold! It worked, all those books I wanted were transferred without a problem! Even 154 MB pdf comic b/w comic - "From Hell"! (although it's a little bit hard reading it, but it's doable nevertheless)
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