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Thanks all for your help.
I decided to convert first, through the command line. The ONLY batch approach I tried that worked is as follows:
start /wait ebook-convert.exe 00001.epub 00001c.epub
start /wait ebook-convert.exe 00002.epub 00002c.epub
start /wait ebook-convert.exe 00003.epub 00003c.epub
start /wait ebook-convert.exe 00004.epub 00004c.epub
start /wait ebook-convert.exe 00005.epub 00005c.epub
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