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A book with a replaceable cover is a *good* thing. It means that should you choose to update the cover for the book in your calibre library resulting in one that differs from that already inside the book, that calibre can automatically substitute it into the book when you Send to Device/Save to Disk or use the Modify ePub "Update metadata" option to replace it inline.
A book with a non-replaceable cover is not necessarily a bad thing. It just means that calibre will not replace the internal cover in those above circumstances. If you have no intentions of giving the book a different cover, or don't care about covers at all, then you will obviously not give a jot about either option.
As to why the counts don't add up to 4080 - how many books do you get displayed when you do formats:epub? My guess is 3966 + 53, not 4080?
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