How to refresh bookmark favicons in chrome

Have you tried clearing the cache then restarting Chrome? Try that first. If it doesn’t work, then you’ll have to force it as follows.

1. Close Chrome
2. Open your User Data folder
3. Delete the Favicons file
4. Run Chrome
5. Visit sites to force the icons to be re-downloaded

Did you try to force the refresh when you are on the page and press Ctrl + R?

[EDIT] (Credits to James, see his comment) try to refresh and empty the cache with Ctrl + Shift+ R

[Source on Google Chrome Help Forum]

My issue was that despite deleting the favicon for a locally hosted site, Chrome still displayed it.

This comment on a Chromium issue says:

Favicons are not stored in the cache, they're stored in one of the SQLite databases. So they don't get cleared with the cache. This is a good thing since all your bookmarks would lose their icons until you visited them again.

This explains why clearing my cache did not solve the problem.

Here's what I did to clear the favicons for my site:

1. Closed Chrome in order to release its file locks
2. Downloaded the appropriate SQLite command-line shell for my OS
3. Extracted the archive
4. Opened my user data directory
5. Deleted the Favicons-journal file
6. Copied my Favicons file into the same directory as the SQLite command-line shell
7. Opened Command Prompt
8. Changed directory to that which contains the SQLite command-line shell
9. Executed sqlite3 from Command Prompt
10. Ran the SQL which follows this list
11. Moved the Favicons file from my SQLite command-line shell directory back into my user data directory

.open Favicons

DELETE FROM
    favicons
WHERE
    id
IN (
    SELECT
        icon_id
    FROM
        icon_mapping
    WHERE
        page_url
    LIKE
        '%localhost:%'
);

DELETE FROM
    favicon_bitmaps
WHERE
    icon_id
IN (
    SELECT
        icon_id
    FROM
        icon_mapping
    WHERE
        page_url
    LIKE
        '%localhost:%'
);

DELETE FROM
    icon_mapping
WHERE
    page_url
LIKE
    '%localhost:%'
;

Adjust this to suit the URLs which you wish to clear the favicons for. In my case, the targeted URLs were along the lines of http://localhost:8000/.