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Zynster; when I read the help for calibredb remove it tells me it expects another argument; a comma separated list of IDs of books to remove; NOT a list on stdin of books to process, so I would not have expected that to work at all.
You could also just have dropped the zero byte files at the OS level and then performed a library check function to identify the missing material in calibre and then had calibre peform a cleanup.
Also, in the calibre gui, did you try a search for
size:=0 format:mobi
then select all the displayed records, right click them and do either a remove books | remove selected books OR a remove books | remove remove files of a specified format and select mobi?
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