Normally the thumbnails at the new tab page are organized by how often you visited a page.
But after removing such a thumbnail by clicking the little gray cross at the right top corner deactivates the logic for this page on the whole. The page is added to an internal black list.
So the idea to visited the site often enough newly does not work to show the thumbnail from this page again.
So we have to choices:
- reset the black list
- remove an entry from the blacklist
Reset the black list
By removing another thumbnail from your “New Tab” page you will get a toolbar at the top with the option to restore all thumbnails

Removing an entry from the blacklist
In newer versions of Google Chrome you will find the black in the preferences file themselves. This is located under “%LocalAppData%\Chromium\User Data\Default\Preferences”. There are a section “most_visited_blacklist” to configure the entries. But till yet I does not investigate the logic behind the notation there.
It seems that in older Version was an stand alone file for that (“%LocalAppData%\Chromium\User Data\Default\most_visited_blacklist”).