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I transfer via Calibre and use the extension KoboTouchExtended to convert to kepubs while transferring. I've learned to check the "silently ignore failed transfers", and transferring in small batches, then splitting the batches that failed. And at the end I manage to transfer everything, though it is long and painful (I have some 4000 books on the Forma). I wonder whether there is a way to do something similar with your problem.
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