From MozillaZine Knowledge Base
This article will help you recover bookmarks that may be missing when you upgrade from Firefox 2 to Firefox 3, if you ever used Firefox 3 in the past. To recover bookmarks that may be missing for other reasons, read Lost bookmarks and Bookmarks not saved.
If you ever tried out Firefox 3 (including a pre-release or Beta version), went back to using Firefox 2 and then upgraded to Firefox 3, any bookmarks you added since you went back to Firefox 2 will be missing, if you used the same profile for both versions. This happens because Firefox 3 uses the places.sqlite file to store both bookmarks and browsing history, while Firefox 2 stores bookmarks in the bookmarks.html file. Firefox 3 will only convert the bookmarks.html file to the new "Places" storage system the first time you use it. 
As a first step, exit Firefox and restart the computer, then reopen Firefox to see if the issue is resolved.
- Note: If you use Norton 360 2.0 and you see your bookmarks when you first open Firefox after restarting the computer but all of your bookmarks are missing when you later close and reopen Firefox, this is a known issue (bug 452469).
If your bookmarks are still missing, close Firefox completely and then use one of these methods:
Manual removal method:
- Open the Firefox profile folder and remove the files places.sqlite and places.sqlite-journal, if present, and localstore.rdf to another location (or rename, e.g., to "places.sqliteX" and "localstore.rdfX").
- Open the bookmarkbackups subfolder and remove any .json files to another location (or rename).
- Restart Firefox. Firefox will then automatically import the bookmarks from bookmarks.html in the profile folder.
- Restart Firefox in Firefox Safe Mode then select "Reset bookmarks to Firefox defaults" and click "Make Changes and Restart". Warning! When Firefox restarts, you will not see any of your bookmarks.
- In the Firefox menu, click "Bookmarks -> Organize Bookmarks -> Import and Backup -> Import HTML..."
- Choose the default, "from an HTML File" and click Next.
- When the file picker appears, navigate to the "bookmarks.html" file in the Firefox profile folder. If you cannot find this file, read Show hidden files and folders. Note: On Windows, you can type "%APPDATA%" in the file field and press Enter, then go into Mozilla, then Firefox, then Profiles, then xxxxxxxx.default (where xxxxxxx is any sequence of numbers and characters) and select the bookmarks.html file.