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I have a desktop which has one system drive and one HHD. I used VeraCrypt to encrypt the system drive.

Does it mean that VeraCrypt also protected my HHD (my second drive)?

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No. If you only encrypt the system drive, the other disk units will not be protected. Many systems allow to boot from a removable media (CD/DVD or USB memory stick). It is the standard way to recover some data after a system disk failure.

But if an attacker manages to boot from such a removable media, all non encrypted disk will be unprotected.

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System drive means the drive the current operating runs from.

For the second one, you could use an encrypted file container, which is convenient and useful if you also want to back it up.

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