I don't know what I did right, but I'm using calibre to copy mine over as well, but I'm doing it batches at a time. So far, I think it's missed adding a title to the right collection only once, and they're all in the correct series order, too.
Then again, I've just spent the last month sorting and adding my books to Calibre, adding metadata as I go, so maybe it's all that work that's now paying off.
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