Browsers don't necessarily store favicons in the cache like other web page data, and it can take a while before they get around to updating the favicon for a site. For example, Safari stores them in the ~/Library/Safari/WebpageIcons.db file (on an OS X system), so you can force it to reload favicons by deleting that file. (You should probably quite Safari first.)
I don't know much about Chrome, but there's probably something similar you can do.
EDIT: Got curious, so I went ahead and googled it. Try this out:
http://www.chromestory.com/2015/04/how-to-refresh-bookmarks-favicons-in-google-chrome/