I don't see any choice but to reinstall Windows' bootloader. Use the
fixmbr utility that is available from the Recovery Console.
But I wouldn't trust fixmbr to save your partition table if I were you though and I'd make a backup of the MBR with
dd(1) just in case.
For using the NT loader to dual-boot,
this might help.
Since I've never used Truecrypt, I can't tell how it works, but I doubt it'll understand and encrypt the FreeBSD slice. However there are other methods available on FreeBSD for encrypting disks.
Oh yeah, and Truecrypt is a true POS for requiring the Windows bootloader. Sorry I couldn't resist.