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So I was attempting to encrypt my (Windows 7) system drive with Truecrypt and it stopped at around 15% and said that there was a segment error and that it could not proceed until it was fixed. So, I restarted the computer and ran HDD Regenerator which subsequently fixed the bad sectors on the drive, but now my system cannot boot.

So, I run a number of recovery disks to no avail (Windows repair is unable to fix) and the drive won't mount on a linux version run from a CD because the drive is encrypted. So I tried mounting the drive using Truecrypt under the Linux distribution on the disk and selected "Mount partition using system encryption without pre-boot authentication" so I can decrypt, but I get an error message about it only being possible once the entire system is encrypted.

How do I get out of this mess? I need to be able to back up the data that's on that partially encrypted drive so I can reinstall my operating system.

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Unfortunately in this case there's not much you can do, once a truecrypt partition is corrupted, it's impossible to repair, due to the nature of being encrypted.

I would also be careful with your HDD, some sector might be damaged, since it's generating a segment error, I would format the hard drive and try one more time, if it is still generating an error, then I'd stop using this HDD, it's a bad HDD.

Also, when you need to encrypt anything, you have to back it up somewhere, there's always the risk of corruption, and when that happens, you lose 100% of the data on a encrypted partition. So it's an extremely bad idea to not back up.

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Proper encryption allows for absolutely no recovery from such events. It truly is what you want. So, never lose encryption keys and store backups separate from the system to aid in recovery if you have drive failure or file system corruption. –  Fiasco Labs Nov 25 '12 at 16:49

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