Are you sure that they have exactly the same URL, symbol by symbol, up to the very end? Otherwise you might need to use the “Expert mode“ to ignore different aspects of the URL or to use another criteria than the URL to determine duplicates. However, I would not advise you to do so unless you exactly understand what you are doing in this mode, as this might consider much more bookmarks as duplicates than you would like to.

Reply to your reply: By design, the extension does what it says, namely removing duplicate bookmarks. If you want something else - removing *similar* bookmarks - you can get this feature in expert mode; but it lies in the nature of things that this is a very dangerous feature. Especially if you do not understand exactly what is "similar" by the regular expressions you chose, chances are high that you remove bookmarks you actually wanted to keep. If it worked for your use case, that's fine for you, but unless you re-check very carefully manually, chances are high that you remove too much this way.