Truecrypt system encryption of Windows partition uses first 512 b (sector 0 – MBR) for the bootloader, next 2048 b (sectors 1–5) should be used for decompressor SW and next 29 184 b (sectors 5–61) as the compressed Truecrypt boot loader. Considering the hard drive geometry to pretend having 63 sectors per track, the last sector of the first track (therefore sector no. 62) contains the system partition volume header. (Very important, because without it the partition cannot be mounted. For non-system encrypted partitions, the volume headers are backuped at the beginning and end of the partition.)
UNIX traditionally supports so called symbolic links, created by the command “ln –s”. On Windows, however, it is still largely an unsupported feature, although the NTFS filesystem specification allows to create symlinks and from Vista on, the default directory structure also uses some symlinks to keep backward compatibility for older programs utilizing directories like C:\Documents and Settings (pointing to new C:\Users) etc. There are some command line tools like Junction and Mklink, a great context menu tool called Link Shell Extension and also a listing tool NTFSLinksView. The major problem is that there is virtually no backup tool or compression software that would support this filesystem feature. Finally I found maybe the best solution available today, which is CYGWIN and TAR, that saves absolute paths starting with /cygdrive/ when (Win2000+) Junctions are used, and relative paths when (Vista+) Symlinks are used. Unfortunately, the same tool cannot restore the native NTFS symlinks when decompressing, it makes the symlinks useful only for Cygwin environment!