The bookmarks are already in there. That Bookmarks folder is the one on the bookmarks toolbar. There is no access to the parent directory of the bookmarks toolbar any more. That is the problem. The Bookmarks on the left at the top of the list is just a line of text, not the parent directory. The parent directory is simply not available to add things. Once you take everything out of there except the hard-wired directories, there is no way to get back.
I was wondering if putting most of the bookmarks back into the parent directory would make it possible to use the "Add to Bookmarks" menu item again. It does not work with Opera 56 or subsequent versions. The doorhanger that drops down from the heart symbol is totally blank.