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What is the source format? is it Mobi or is it ePub? If it is Mobi, you need a Windows machine to have a look at it. And if it is Mobi, there is no reason for the duplicated lines. Is your Calibre updated so you can convert to ePub? maybe your install is botched. I cannot say. Try using Windows and see what happens.
If the eBooks are ePub to star with, do not use Calibre. Take the copies that have not been put in the Calibre library and move them to your 650 using Reader Library. Maybe it's a problem with Calibre. I know Reader Library will not change your ePub in any way when moving to your 650. So try it and see.
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