Janet,
I definitely unplugged the USB drive before I performed the upgrade because I didn't want to risk the integrity of the data that was on it. After the upgrade, during the first reboot, I plugged the USB drive back in and it said that the disk hadn't been checked in 537 days and it was forcing a check. I waited that out and the bad superblock error showed up after loading udev (I think). I rebooted the machine and it proceeded normally to a login prompt so I dismissed it as perhaps a temporary glitch.
Then, after getting yum to run, I had to reboot again and that's when I got stuck and couldn't get past the bad superblock error.
Output of df -h is:
[root@mail ~]# df -h
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/main-root
266G 177G 76G 71% /
/dev/sda1 99M 20M 75M 21% /boot
none 4.0G 0 4.0G 0% /dev/shm
/dev/sdb1 917G 230G 641G 27% /mnt/affa
Perusal of the contents of /mnt/affa look as expected, so hopefully everything is OK. Will know more when AFFA runs tomorrow AM.