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I can see how that could be an issue, but if that were the case, then wouldn't Calibre show the deleted formats still when I select a book? In these cases, I can select the book, choose edit metadata, and the 'formats' box is empty.
I didn't actually go through and manually delete these books with explorer, but rather used a dup finder app. (Essentially the same effect though.) Any files with matching md5 it deleted all but one of. Since I had imported from multiple ebook directories into calibre, there were a lot of duplicates.
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