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I seem to remember it coming up elsewhere that the calibre tools do not play well with batch files. The symptom being what you state - that subsequent commands do not get executed because the command processor dies.
I seem to remeber that the best answer that anyone came up with was to that when you wanted to execute a new command you did it in a new instance of the command processor (using the CMD /C option).
Another solution was to use alternative command processors.
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