http://www.srcf.ucam.org/~cjk32/hdcd/
According to the discussion (here) the following command should work:
hdcd.exe < 16bit.wav > 24bit.wav
or
flac -d -c hdcd_orig_16bit.flac | hdcd | flac -5 -f – -o decoded_24bit.flac
or
flac -d -c hdcd_orig_16bit.flac | hdcd | flac -5 -f – -o decoded_24bit.flac