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I was thinking of encrypting the whole disk or only my data partition D:. However, I have NTFS junctions on the system partition C: linking to D:. More precisely, I made a junction to point my user profile directory to a directory in D:, effectively storing my user profile on the other partition.

My concern is, if I encrypt D:, my user profile cannot be loaded before mounting it with TrueCrypt, which may require logging in my account which cannot happen before mounting the partition.

Is it actually possible to encrypt D: and be able to use Windows normally in this case? Any other ways other than performing a whole disk encryption?

Edit: I don't have my system partition encrypted. If I have to, I would rather encrypt the whole disk.

I also have Ubuntu installed on the extended partition, which is not encrypted either.

share|improve this question
Is your system partition encrypted? If it is then you could encrypt D: and configure it as a System Favorite Volume. – gm2 Mar 26 '13 at 6:29
@gm2 No. If I have to encrypt the system partition, I would rather just encrypt the whole disk. – Alvin Wong Mar 26 '13 at 6:59

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