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The add-to-library was never intended to do mass uploads. You are using iOS CC so I can't go further than that.
Adding a book to the library via CC doesn't give you covers or CC metadata because the device interface doesn't support that. However, the metadata should be in the book itself because unless you explicitly turned it off, calibre updates the metadata in the book when it sends to the device. Try saving a book to disk then adding it to calibre, ensuring that the calibre option Preferences / Adding books / "Read metadata from contents rather than file name" is checked. You will get the best results from epub and azw3.
It would be better if you could copy the book files from your device to the computer. Is that possible with iOS? If so, then you can do the copy then add in bulk.
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