The Backup tool can back up all files in a partition, even if you do not have Read permission for the files. However access rights are preserved. When the files are restored, the access settings are maintained and you are unable to read the files.
Backup can also back up files that are encrypted using the Encrypted File System (EFS). These files are stored in encrypted format on the backup media and are restored in an encrypted state. Or, you can send them to a designated EFS recovery agent for recovery if the owner of the file has lost the certificate required to decrypt the files.