I opened a ticket sometime last summer (I'm afraid I don't recall the number) at your request, suggesting that it would be useful to have the option of "adding a new format to an existing book" when dragging a new book to Calibre. I suggest that Calibre could offer three choices when it detected a duplicate:
1. Overwrite the existing book.
2. Add as a new format for an existing book.
3. Add as a new catalog entry.
I think that's essentially the same as the previous poster is asking for here.