This happened to me a while ago with firefox,Sadly never got them back and had to start from scratch as I remember.Does help if you occasionally back up your bookmarks just in case.
Well, I've found the bookmarks and copied & pasted them somewhere safe so losing them is no longer a worry. FF seems to keep backup copies which go back 5 days. That is a huge relief. It is a complete PITA not having bookmarks, even for regularly visited sites.
The bookmarks are in the file "bookmarksbackup.default" in w1ld78xa, which is the only file that comes up when I run c:\Documents and Settings\XXXX XXXX\Application Data\Mozilla\Firefox\Profiles\
I now can't open Firefox. Everytime I try I get the message "Firefox is already running but it is not responding. To open a new window you must first close the existing Firefox process, or restart your system."
I've restarted several times with no joy. I've also uninstalled FF and reinstalled the latest version but I still get the same message.