I received your reply via email and wanted to respond here because the issue may be of interest to others.
When you backed up your old device to your iCloud account, I would have presumed that when you connected the new device to your iCloud account, the files would have been placed into the proper location on the new device.
Unfortunately, I can't diagnose what might have gone wrong with the backup/restore process. I do have some additional questions for you.
Do you still have the old iPad? If so, are the files still there?
If the files still exist perhaps we can try to synch the two devices again via iCloud, or try some other measure to move files from old to new.
Sorry I'm not able to issue a more definitive explanation (yet).