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Can I encrypt single partitions in an otherwise unencrypted disc?

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I am not sure what you are asking. Windows bitlocker of other system allows you to encrypt a single volume associated to a partition on a disk.
If you try to backup within Windows with that partition locked, ATI will complain. If it is unlocked, ATI will backup the partition in as decrypted information. If you try to backup from the recovery CD, it won't work. You would have to do a full disk backup sector by sector.