You can backup and restore a TrueCrypt system partition if you use imaging software that is capable of reading and writing in raw mode -- copying the whole partition byte for byte without regard to the underlying file system. You also need to back up the MBR (master boot record), and perhaps the data between the MBR and the first partition.
And you must not image it when running Windows, like with "hot running" image software such as Acronis TrueImage. You must boot from a separate disc (CD or external drive) with your imaging software and then take the image.
I used Clonezilla to back up and restore a Linux encrypted root partition and MBR; I don't see why it shouldn't also work with a TrueCrypt encrypted partition.
Sometimes the problem is only with the header of the TrueCrypt partition, and restoring just the header might solve the problem. TrueCrypt provides the ability to backup and restore the header (you'll need to boot with the TrueCrypt rescue disc or another Live CD to restore the header).
Which software did you use in your backup and restore attempts? I would recommend Parted Magic, which is a Live CD that contains disk imaging and partitioning utilities (including Clonezilla), and also includes TrueCrypt.
Not while encrypted, no. – None – 2011-07-19T04:56:18.660
so then truecrypt essentially prevents anyone from imaging a drive and investigating it lively? – nobody – 2011-07-19T05:00:55.260
Effectively, yes. It also allows the partition within a partition which makes a good dummy if someone gets hold of the first password. – None – 2011-07-19T20:08:14.267