After you use the built-in restore feature, copy the trophy folder back into the correct user name folder. You will than need to rebuild database and you will have all your trophies back. You can rebuild database in the recovery menu, when you ps3 off just hold the power button down til you hear the 2 series of 3 beeps.
Actually its possible to backup trophies. you will need to either ftp or use a filemanager to backup your home folder to your external. when you open your home folder you will see folder with #s like 00000001, 00000002, etc, open the one is for your username, you can check this by opening the localusername file using a text editor. Inside you will see the trophy folder.