It didn't write the new save folder until you opened the disk with the new name.
Save folders are also configuration folders. That's why you'll notice that if you re-open a game you've already opened, it just starts right up without annoying you again with the config settings.
The emus don't delete save/configuration folders unless you tell it to (by pressing black or white, whichever one is not the favorite's button, and then confirming when prompted). If you had saves for Final Fantasy 7 that worked before, they must still be there under whatever name you used to call the CD.
Assuming you didn't accidentally delete them within the emu or in an FTP session (which should be fairly hard to do on accident), all you have to do is find the old config on your box, delete the new config, and then rename the old one exactly like the new image name and they should all still work for you.
Hope that helps,