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ShadyK I just ran into the same issue. But it was only one Top Hit I wanted to delete. What I eventually did was go to the page that I wanted to delete from top hits. Then I went to Show History in the History menu. I highlighted the item I wanted to delete, right clicked, and hit "delete."
Now that URL never autocompletes when I start typing it. It seems this will work for any URL you want to delete from your Top Hits/URL autocomplete. I imagine that deleting your whole history will delete all autocompleted URLs, but I don't want to test that becaues I want most of my autocompletes.