OMG I was just about to ask the same question. I've been tearing my hair out trying to get this working. It wasn't making too many mistakes, then suddenly messed up an entire series (replacing one book with another, replacing some books by their omnibus edition or even a multiple book special offer...).
I wasn't always doing them in bulk either. Right click on a book, edit metadata, download... Seems like the logical place to do it from. Spent ages trying to find a nonexistant option so it would let me choose. Didn't occur to me that it might work differently if I opened up the individual metadata window.
I honestly think that could do to be changed, at least put a message in the confirmation window that the metadata and covers downloaded can be selected individually in the metadata editor window. Otherwise people just won't know to go through there.
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