I'll try to give a few answers but some one else may have better advice.
As far as Calibre is concerned you can delete any duplicates within Calibre and they will not be deleted from your hard disk, just within that application.
For Calibre to convert your Sony lrf and epub books to mobi (used by Kindle) they must not have any DRM copy restrictions. To remove DRM is another subject and topic.
I would not convert any lrf or eboub books to pdf to use on the Kindle. Convert that type of book to mobi for best reading results. Books you already have in pdf should be able to be read on the Kindle.
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