That's what I thought you might have meant. Obviously, as you have figured out, the data is not really deleted. When you mount the second HDD at /home, there is nothing to "see" because there is nothing on the second HDD. Copying what exists under /home on the first HDD to the second HDD will resolve the problem.
Even if you can't login as root from GDM, you should be able to switch user (su) to root in a terminal. Open a terminal and try this
mount /dev/sdb1 /mnt/sdb
cp -Rpv /home/* /mnt/sdb
mount /dev/sdb1 /home
You will prompted for the root user password after the first command. Replace /dev/sdb1 and vim with the appropriate device and your favorite text editor. When you edit /etc/fstab, add a line similar to the one in my first post to make sure your second HDD mounts at /home every time you boot.