Not sure if this has been documented before, but I found an error that couldn't be fixed with calibre's EPUB to EPUB conversion. If the NCX has target with #hash to the ID of <body> in the target document, conversion will fail with unresolved hyperlink. Tested with Kindle Previewer 3.66. AFAIK this only happen in NCX file --- linking with <a href=""> inside HTML is fine.
I am thinking of improving
https://kindle-epub-fix.netlify.app/ to handle other kind of common problems so I am investigating various problematic EPUBs.