Ah - perhaps what happened was instead of backing up the files, you accidently moved some of them.

Write down the names of all the files on a piece of paper next time before you back them up. After you back them up, compare your list of files on the piece of paper you wrote to the files that are in the save game folder, and make sure they are all still there.

Perhaps we can help you figure out what went wrong with the backup you did so it does not happen again - describe in detail everything you did when you backed up the folder (what folder were you in, what keys did you press, what did you click on, etc)?