Disclaimer: No claim, explicit or implied, is proffered that I really know what I am talking about.
When I was doing the interface art and table entries for the GVF Reshef that Aldo modelled, I also gave the ship its final name, and had to rename the pof and all the maps accordingly. In PCS there were a large number of texture files referenced, and I had to reidentify all of these textures with their new names. Some of these textures listed in PCS did not seem to correspond to any extant files, but were included and necessary anyway. Perhaps those references are used for such purposes as this.
So anyway, the point of my rambling is this: Use PCS and make sure that all textures listed for your ship are referencing the new textures you have made.