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If i install ubuntu as normal on the secondary HD, is it going to over write MBR/true crypt and screw up my main windows install?

Any help appreciated!

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Yes, it will. I believe the only way to go about this is to fully decrypt the disk (using TrueCrypt in Windows), install Ubuntu dual-booting, and then set up full-disk encryption again. I believe TrueCrypt has native support for encrypting multiple operating systems now, but I am finding oddly little information about this online.

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This is correct -- I recall reading this in the TrueCrypt documentation, although I'm in a rush at the moment and can't find that reference. The process is simple, though: 1) Decrypt the Windows disk. 2) Install Linux on the second disk. 3) Re-encrypt the Windows disk; during this process, TrueCrypt will ask if there are additional OSes installed, to which you will say that yes, there are. Not sure what the process after that is, but the wizard should take care of you just fine. – Kromey Jun 9 '11 at 1:19

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