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@eboyhan: I don't know about books from amazon as I dont have any, but I tried changing the metadata on a side loaded book and resending it to the kindle and the collection weren't affected. Judging by collections.json the collections are keyed to absolute paths, so changing file metadata should not affect anything as long as the path does not change. Of course if you change the title/author, and resend using calibre, the path will change.
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