Well, unless something about your sorting mechanism is weird, sorting the subset by the same rules as the superset should produce a properly sorted set.
Comment on Re: sort an array according to another array
The sorted array is produced by a combination of several external applications and is the ultimate result of an initial data set of several hundred megs - a few weeks of work. The sorting of the smaller set is something I need to do quite often, there is just no way to repeat this process every time (nor any need).