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I've been studying ISBNs for software I'm writing, and there are indeed limitations in what it can identify. The strongly-suggested use is to have one ISBN for every separate edition of a book. But a single ISBN may refer to different printings, even with different cover images. Or in a different size. When talking about the "same" edition, it usually means roughly that between the two physical books each chapter starts on the same page in both copies. (This allows for fixing errata between printings.)
I think ISBN will always be limited in this way, and ISBN International should come up with additional codes for identifying unique printings, and possibly for identifying unique 'works' where the text is the same but the pagination may be different. But trying to tie that to ISBN would over-complicate a very simple code intended for use by booksellers.
In the mean time, in my software I just invent UUIDs for identifying individual printings and specific works; if a new numbering system came along, I could integrate it quite easily, but in the mean time dumb identifiers serve the same purpose for local catalogues.
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