I just finished the upgrade and on my first game I got my highest score ever
Anyway, a few tips:
1) Use an 8GB USB (SanDisk works). Anything larger or smaller doesn't seem to work. If you insert the USB into the update port and reboot The Hobbit and it doesn't immediately start the update process, try another USB.
2) Make sure the USB is formatted FAT32 and not NTFS. Writing the files to the USB seems to stop for about 5 minutes. Just give it a chance to finish.
3) Back up your config first. If you don't, it will be overwritten by the defaults. Also, all of your high-scores will be gone.