The page count by chapter is an exact calculation of how many screens you have to 'turn' for that chapter. The page count by book is an estimation. (though in my experience, a reasonably accurate one,, most page turns for me come out to 1 page,)
This is necessary, otherwise, the kobo would have to render the entire book every time any of the formatting options are changed to re-calculate pages. (And with no limit on the size of books, that could quickly become a *very* demanding task.)
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