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Each different paper edition has a different ISBN. If an equivalent ebook has an ISBN (it might not, they don't need them) it will always be different from all the ISBNs for paper editions.
I makes sense to "merge" different electronic formats that have the exact same content (like conversions). Really Calibre is a Catalogue, not a library, when anything other than ebooks that transfer to an ereader is considered. PDFs versions of a real ebook are a special case and PDF only versions are a special case.
Better to keep paper & electronic entries separate. I'd even have separate entries for different paper formats, never mind different editions.
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