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So, why are some books topaz and some books mobi? Is topaz supposed to replace mobi at some point as B&Ns new eBook standard?
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B&N doesn't sell mobi's
or Topaz books. If you mean Amazon, then no... Topaz is not intended to replace mobi. I think Topaz is a quick and dirty solution to get scanned books into an ebook format. It also has its uses for books that contain lots of mathematical formulae, tables, inline images and such. Topaz lends itself well to any highly formatted layout such as poetry that can be a nightmare for mobi to successfully recreate, as well.
But unfortunately, Topaz usually sucks to convert
to any other format. You will lose italics and bold formatting in the process. And since the conversion process can only use the (usually uncorrected) OCR of the scanned book to recreate the text, results can be anything from "Not too terrible" to "really, really sucks." ...Without a lot of TLC, that is.