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The merge behaviour is as you describe. It's intended use is to merge records that are duplicates of the same book with a different mix of formats and metadata into a single record.
You cannot keep different instances of the same format via merge. Calibre only allows one example of any given file type to be associated with a book record.
A possible workaround is to put multiple books into an archive (e.g. .rar) and add that to the book reord.
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