Chrome: remove URL from autocomplete which doesn't show up in history? [duplicate]

Highlight the item (using your keyboard arrows) and use shift+delete

(Note that on the Mac you seem to need to also press fn, so fn+shift+delete)

NOTES

• this won't work on URLs that have been bookmarked. For these you must first delete the bookmark, then delete it from the Omnibar history (you can tell it's a bookmark if there's a star next to it as you start typing)
• you must select the entries in the Omnibar history using the arrow keys to select

Low level answer, if you want to know the whole list:

This is stored in an sqlite3 database in Google Chrome's userprofile folder, on Linux it's located in

~/.config/google-chrome/Default/Top Sites

You can use SQLite3 to have a look at it:

me@local~/.config/google-chrome/Default$ cp Top\ Sites ts.sqlite
me@local~/.config/google-chrome/Default$ sqlite3 ts.sqlite ...
sqlite> .schema
...
CREATE TABLE thumbnails (url LONGVARCHAR PRIMARY KEY,url_rank INTEGER ,...
sqlite> select url_rank,url from thumbnails order by url_rank;
0|https://android.stackexchange.com/
...
21|http://archive.org/
23|https://android.googlesource.com/
24|https://android.meta.stackexchange.com/

To answer your question:
You can delete or edit an entry using regular SQL commands, but be sure that Chrome is not running, i.e. the file is not opened (by Chrome). Also note that I did all actions on a copy because of that (was only looking).

I have found several places that mention Fn+Shift+Del for a mac and Shift+Delete for windows.
I do use windows, and from my experience I often needed to use Fn+Shift+Delete.