I'm almost completely clueless about this, but my general thoughts on page numbers in ebooks is that, in an absolute sense, they don't exist. In something like a PDF, yes, there will be absolute pages. But, a KFX/EPUB/etc.., pages will be a product of fonts, font sizes, margins, headers, footers, etc.. Unless all of those are fixed in the CSS/HTML of the book, they'll be changeable in an ereader. So, page numbers will change.
Now, if the ebook has set up page numbers to match a physical book with ids and parts of the spine (? my ignorance is really showing here ?), I'm pretty sure Calibre doesn't rip those things out. So, I'd think page numbers in that sense will continue to exist.
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