Until NTFS write capability under Linux has stabilized, a refresh of the NT partition still entails a reformatting to FAT16 in order to be able to write the NT install files to the partition. NT will later convert the partition to NTFS. Once we get NTFS write capability, we should be able to bypass the NTFS conversion stage and just write the install files directly to an NTFS partition.
So the first thing that is done is that the NTFS partition is changed back to FAT16 so that we can write to it. The the FAT16 partition is formatted. This all happens in the file /auto/jacal/scripts/format.ntinst.pl.