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I have a desktop computer with a small SSD and a large hard drive... as a result, I have installed my windows OS on the SSD but have moved all user data and programs to the hard drive except for "AppData".

My plan was to encrypt both the SSD and HD with full drive encryption and then set the HD to auto-mount so I would only need to enter the boot password. Will this work? I'm concerned that the OS will have problems loading user profiles because TrueCrypt would need to run (and successfully mount the HD) prior to the desktop (and other user files) becoming available.

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I don't know if that's possible in TrueCrypt, but it works well with en.wikipedia.org/wiki/DiskCryptor if you make all drives have the same password and configure auto-mount. Just enter the password once at boot time, and it will mount all drives and partitions that have the same password. It even works on USB drives -- just plug in or switch on the drive, and DiskCryptor mounts the encrypted drive without you having to enter a password, as long as it has the same password as the others. –  Mike Rowave Aug 30 '12 at 4:21

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According to this other question, TrueCrypt can mount two different drives with one password if you choose to have it cache the password.

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