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If I'm remembering correctly, the covers get updated when you make a conversion. Just use the same format for input and output, and the metadata gets updated.
A word of advice, though: PDF is not really an optimal ebook format, some might even argue that it's not an ebook format at all. While I don't want to get into that discussion, you might want to consider using a format like e.g. ePub for any new books you get.
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