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In my experience the first book (file set) you select is the one that calibre will keep. Any formats that are not in this file set will be copied to this file set.
It is well explained that calibre only keeps one file per format in any one given book record/file set.
Best practice is up to the user. Keep both book records or save one to disk or convert the file you want to keep as a dup to another format not found in the record you are merging into. Better yet archive anything yourself you want to be sure to keep.
Difficult for calibre to archive in same directory as both . rar and . zip are valid ebook entries. And as time went on there would probably be multiple files being archived. Not a pretty picture.
Helen
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