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If you have not yet added the books to Calibre (just created the empty book rows), you could turn on the option in Preferences -> Adding books which says that if title and author match to merge into the existing book. Then when you add the books, the formats should merge into the empty books if they are named correctly.
If instead you have already added the books to Calibre and now have duplicates (one for the empty book, one for the "real" one), you can use the merge functionality to first select the empty book, then ctrl+select the "real" one and choose Merge.
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