I just had the case where someone wanted to add a completely new comment on the page, but mistakenly replied to another one. I wanted to fix that and could not find a solution how I can convert it to a standalone comment. A short look into the database table wp_comments revealed the solution.
You just have to set the column comment_parent to 0 for the respective comment and you are done. Hence, if the comment’s ID is 1234, you can simply run the following SQL command:
UPDATE `wp_comments` SET `comment_parent` = '0' WHERE `wp_comments`.`comment_ID` = 1234;