In order to be able to update my reading progress via goodreads integration on a sideloaded book, I have to use the Quality Check plugin to patch-in the mobi-asin. Before Kindle firmware 5.7.2 (which came out a few days ago; I'm on a Paperwhite 3), you could put any ASIN and it would work: paperback, hardcover, whatever. So the fact that calibre just downloads whichever one it finds first was not an issue.
With the recent 5.7.2 firmware, I noticed that now only books that have the kindle ASIN, the ones that start with the letter "B", still work with goodreads integration. So I had to go and change all of the books I had that had the non-kindle ASINs and get the kindle ASINs. So for example, previously it might've been amazon:1491903996 which is the paperback version of a book, and now it had to be amazon:B00PGCMGDQ, the kindle version of the book. I had to re-run the Quality Check plugin to patch-in the kindle ASINs into the mobi-asin fields of each of the azw3/mobi files and resend them all to my device.
Now goodreads integration is working again.
The only remaining unfortunate consequence of this is that: previously, even if a book wasn't available in the kindle store (and thus had no kindle ASIN), you could still get any other ASIN for that book in order to get goodreads integration. Now since it seems to require a kindle ASIN, if the book I have isn't available in the kindle store, it won't have a kindle ASIN, so I won't be able to use the goodreads integration
