If you’re looking for a work-around in the time being, I actually found that I could visit the site I wanted, then go back to the new tab page and change the top sites to show frequently visited instead of favorites.
Once I did that, I could see the site I just visited (you have to ensure you have room on your frequently visited bar for a new site to show up) and then use the pencil icon to click “edit site”.
Then I just renamed it and hit enter, without clicking anywhere else, and when you swap the top sites back to showing favorites, the site you visited and renamed is there.
It is certainly a clunky work-around but it did help me get my favorite sites back.
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