It depends... The Bookmarks Menu has a section called Recently Bookmarked which is not a separate entry -- it's a list from across all of your bookmark folders showing the latest 5 bookmarks. If you delete them there, you also delete the original. (If you want to hide that list, right-click the "Recently Bookmarked" heading and you'll see that option.) Similarly, Firefox includes some special blue search folders on the Bookmarks Menu or Bookmarks Toolbar which show recent activity or some other category. If you do not want to see these but might want to check them in the future, you can move them into a sub-folder so they're out of sight. Otherwise, separate bookmarks should actually be independent so you could delete one without affecting the other. As for why they might duplicate... do you use the Sync feature?