My workflow for "convert book to use on my Kindle Paperwhite that can be marked on my Goodreads account" has been:
1. convert to azw3
2. download metadata in calibre
3. if metadata includes a mobi-asin/amazon ID that begins with B0, skip to step 6
4. open the amazon page in browser
5. switch amazon page to kindle format and find the on the page, copy it to clipboard
6. open terminal and use
the mobimeta utility from the libmobi C library to manually modify the azw3 file's mobi-asin:
Code:
mobimeta -s asin=THECORRECTASIN theactualbookfilename.azw3
Books transferred to my Kindle after using this method will be able to connect to Goodreads the same way as Kindle books purchased directly. The device might replace the cover with the one in the Kindle store, but it won't delete it.
I also find it helpful to run the following, so the converted book will allow me to view it with my preferred fonts on-device:
Code:
mobimeta -s 528=false theactualbookfilename.azw3