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.