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There is no solution in Calibre to do it the way you're trying to do it. Amazon is creating a really screwy mobi file, Calibre hasn't been programmed to handle that scenario, and It's unlikely to happen anytime soon.
If you're seeing that Calibre isn't unwrapping the lines when you use it to convert from pdf to mobi it means that your line unwrapping factor under pdf input is incorrectly set. It seems to be set to zero on a number of user's systems. Set the line unwrapping factor to 0.45, this is the default and generally provides the best results.
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