This one is gonna be kind of hard to fix. Usually, immediately after you delete a website from that section, an option will appear stating "Restore". At that time you can click the option and the site you accidentally deleted will be brought back.
However, that Restore option only last for a few seconds and then you'll never get that option back for that particular site. Also, Google has discontinued the user's ability to manually edit (or put back) a website in that section.
The article I posted below suggested a more difficult way to bring it back, but I've never done it so I can't really put any input on how effective or time consuming this method will be. If you're interested in trying it out click on the link below and scroll down to "Difficult method (for experts) for changing the list of most visited sites in new tab of Chrome":
Espero que esto ayude~