I am not sure I understand what you are asking. I have all my Kindle books in Calibre, but I do not use Calibre to put them on my Kindle. I just download them from Amazon over wifi. I have tried to sideload some books bought from other stores to my Kindle Colorsoft from Calibre and I can read them fine but the covers do not show. So I use Send to Kindle to get other books on my Kindle.
Actually, I have gotten to the point that I only read Amazon books on my Kindle and everything else on my Nook. But I love having multiple readers to play with.
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