[DiapDealer]

And the fonts not working can easily be explained by the paths in the css font-face declarations not matching their actual locations in the archive. Sigil will adjust css urls if they're changed (as long as they're initially correct), but adding font-files to the epub won't set up the initial css font-face rules. If you manually made the @font-face urls point to ../Fonts/xxxx.otf, but the actual font-files were added to the root of the archive (in a non-standard epub), that would explain why 1) your embedded fonts wouldn't render, and 2) why Epubcheck barked about them being unreferenced, and 3) why standardizing the epub structure suddenly made them work. The standardization moved the font files to where your initially incorrect css @font-face rules had indicated they were.

When manually adding urls to xhtml/css, you can no longer assume that font-files will be in a "../Fonts" folder and image-files will be in an "../Images" folder (or that xhtml files will be in "../Text"). They could be added anywhere in a non-standard epub.

You have to either take the time to figure out where your targets actually ARE in the epub archive before manually adding/editing urls to them in xhtml/css, or you need to get in the habit of always standardizing epubs before doing any editing, if you want things to be where they traditionally always have been in the past.