You should not copy books directly into the Calibre folders so that is not the way you should add a new book format. Instead consider the calibre folders like a "black box" that only calibre knows how to manipulate correctly.
What you should do is find the exiting book entry in Calibre, select the Edit Metadata option, and then add the new format from the Edit Metadata dialog. This will copy it into the correct place in calibre with the correct name. It will also update the metadata database correctly.
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