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The way that keeps Calibre happy is to create a simple top-level HTML document that pulls in all the files at the next level in the correct order. You then add this html file you have just created (rather than the individual files) and Calibre will add them all to the ZIP it crates but now the top level file is used to keep the remainder in the correct order.
This works without the need for any changes to Calibre as it is today.
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