Sorry; I missed part of your post.
If you go into the default folder, you'll find a file called "bookmarks.html". That's the file that stores your bookmarks. Save this, delete the rest of the default folder, and let Firefox make a new default folder. Once that's done, quite Firefox and replace the new default folder's bookmarks.html file with your old one.
It is very important that you quit Firefox before replacing the bookmarks.html file. Otherwise, it will overwrite the file with the bookmarks it had when you quit it -in other words, the ones from the old bookmarks.html file- and you'll be stuck.