Well this is promising

A quick look through a .pc.naf file shows that where the "DDS" file format marker is for each texture immediately before it is a 32 bit number which is the length of the texture.
This means I may be able to simply split the file up into texture and non-texture chunks and then rebuild with different sized texture chunks and have it all just work.
More than likely though there are other length values or pointers to elsewhere in the file that would need rewriting but at least I have somewhere to start.