Remove favicons from Safari's cache
Safari caches the favicon for a site the first time it views it, even if the site doesn't have a favicon. This means if one is added later, or it is changed, you'll need to manually remove the cached file. This is pretty simple for a single site:
Then, just remove all the files that match.
grep -r "domain.tld" ~/Library/Safari/Icons/
Then, just remove all the files that match.