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Did you first check the file before putting it into calibre to ensure it wasn't missing content. Calibre doesn't alter content by adding a book to the library. So if it's missing it's probably the automator file didn't properly add all files.
A second possibility is all of the content is there but the automator file didn't create a separate section for each input file. It could have only split when the file size reached a certain amount. Say the average file size is 10k and it's going to make each section within the book 100k it could be packing about 10 files into a single section.
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