by Howard Miller.
Yeh - moodledata is a critical part of the backup. There's no real point backing up the Moodle program files as you can always download those again.
The files you are seeing are what files now look like in Moodle 2, so the file conversion appears to have taken place. However, I'm not sure this helps you. The files now have vital data in the database and if this part of the process has gone awry you still have a big problem.