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I believe that there can be some strange interactions between the Windows command line processor and Calibre. The effect is that the batch file tends (as you found) to get abandoned after executing a calibre command. Using the Start option to run the commands should get around this although you might want to also use the /wait option as well on each line after the Start keyword to make sure each one runs to completion before the next one is started.
Alternative Windows command processors seem to not suffer from this issue so it is not clear why the default Windows one does.
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