Recently I had a problem with my bookmark favicons(favicons of the bookmarked sites) in Google chrome. I searched in Google for the same problem. Some sites recommended (for windows OS) to go following address of your computer
“C:\Documents and Settings\Administrator\Local Settings\Application Data\Google\Chrome\User Data\Default”
And delete or rename the “favicons” file. I did but not got the result. My bookmark favicons remains same.
Now I got a simple solution for this problem. Simply visit the bookmarked link and remain there (in the site) for some seconds. Then the favicon of the site will reappear in the bookmark in your Google Chrome browser.
Hope this will help you to solve your missing bookmark favicons in Google Chrome problem. As I have searched in google forum many have reported the same problem but there were no proper (instant) solution.