Try and look if firefox didn't just create another profile.. Click start, run and type in "%AppData%\Mozilla\Firefox\Profiles" (without quotemarks) to goto the folder where firefox stores all of ur settings an stuff.. If firefox created other profile(s) there will be more than one folder there(they have strange names like doscvp82.default) have a look inside these folders(profiles) and look at the bookmarks.html files inside the directory's untill you find the one that went missing.
If you find it, make sure you close firefox, then go start, run again and run the command "firefox.exe -profilemanager" again without the quotemarks, and then select the profile that u found in the appdata folder..