Hi there!
To remove all your duplicate bookmarks at once, it is easier to do it in Chrome with an extension. First, if you are using Safari, export all your bookmarks. Open Safari, and click File on the top of the screen. Next, click Export Bookmarks. Save it to a folder you can remember. Afterwards, install Chrome, and search Bookmarks clean up. Install the extension. Then import your bookmarks to Chrome by clicking Bookmarks on the top of the screen and then Bookmark Manager. On the right side of the screen, click the three dots, and select Import bookmarks. Then click the puzzle piece on near the top of the browser, and select Bookmarks clean up. When that opens, click Find duplicated bookmarks. On the bottom of the screen, press Select in same folder. Then click Remove all selected. Go back to the Bookmark Manager, and click the three dots to export your bookmarks. Open Safari, and import those bookmarks by pressing File and then Import From and Bookmarks HTML File.
Hope this helps!