Ok, something odd is definitely happening.
As I stated, I found something that worked for me as a workaround for this whole cover issue: I converted my epubs to mobi, and in calibre's mobi conversion output I chose "both" under "Mobi file type" and also checked "Enable sharing of book content via Facebook, etc". This made tagged the files as PDOCs by my Kindle while preserving the covers; pagination and other AZW3 features.
However, as I found out today, since the Kindle tags the file as a PDOC, the word builder feature which I use extensively doesn't work.
So I tried something else. I picked up these Mobi files I converted in the way described above and further converted them to AZW3 files. I tried this with two books, and it did work. They rest in my Kindle tagged as ebooks, with the embedded cover preserved and with all AZW3 features, including Kindle's word builder function, working sound.
Nonetheless, further tries were unsuccessful. I kept trying doing the same process with other ebooks, but my Kindle kept replacing the covers. Why would it work with some books and not with others? Maybe it has something to do with embedded metadata? I found that one of the books for which this procedure didn't work has some UUID identifier. Maybe is this related?
Any suggestions?
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