ISSUE
You choose to restore items from a Client Agent based File Level backup and you find that there are entire folders that are missing from the backup.
RESOLUTION
You must add the Local System account (also known as NT Authority\System) to the folders that are missing. Once this has been done and verified, run 1-Time Full of the Protected Asset (Client) which will now contain the missing data and correct the backup chain from that day forward.
CAUSE
The Local System account has not been given Full access to the folders that are missing.