I'm not sure that it's possible to download the books from iPad to PC. Calibre Companion is for UPLOADING the books to the tablet or phone, not the reverse. Maybe if you use CC to connect as wireless device to Calibre running in your PC, then Calibre will be able to treat the device as a external storage and grab the books, but I haven't tried, that's not what it was designed to do. Given the tendency of Amazon to obfuscate its content, probably you'll pick a binary file that you won't be able to read.
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