Hmm, that's odd. Is it set to auto update? If it is turn those off.
Okay... this may help. Apparently Firefox backsup bookmarks everyday, I'm not sure if this is entirely true but I'm hoping for your benefit that it is.
Quote:
Important: Windows users should make sure they can view and search hidden files and folders as the profile folder containing your stored bookmarks is hidden by default. To locate bookmarks files anywhere on your computer, you can use your operating system’s file and folder search feature to find bookmarks* (be sure to include the asterisk, with no space). You can open any bookmarks file in HTML format from within your Mozilla browser, by using "File -> Open File" from the menu to check its contents; links in a bookmarks file opened in this way will be clickable (see this article for details).
[LIST][*]In Firefox 1.5 and above, five daily bookmark backup files are saved in the bookmarkbackups folder, located in the Firefox profile folder. You must recover one of these five backups before they are overwritten by newer versions.[/LIST] [LIST][*]In Firefox 2 and below, and in other Mozilla browsers, bookmarks are stored in the file "bookmarks.html", located in the profile folder. There is also a "bookmarks.html" file in the program folder, but this one is only a template and does not hold your bookmarks. To make sure you have the right file, you can open the bookmarks.html file or any bookmark backup file using "File -> Open File" from the menu (see above).[/LIST]
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If that brings them up then we should be able to restore them back to where they should be.
**Crosses fingers for you**
Let me know if you find it and I'll look to see how to restore them.