all calibre does when sending books to the kindle is copy them over and update the metadata inside them. If the file is there ont he kindle andhas the correct size, then basically calibre has done its job. The rest is up to the kindle's indexer. The indexer often crashes/fails silently on some books. Usually converting them again either to azw3 itself or MOBi will fix the indexer issues. But note that if the indexer crashes it wil lfail to index any book that is *after* the problem book in its list. So yo uhave to identify the problem book correctly.
See
https://manual.calibre-ebook.com/faq...id-not-show-up