I think it has to be in an fpk file, because I can't find anything art-wise in the full mod that would have changed the terrain graphics after an hour of searching. I'll give that a shot and report back.
You were 100% correct. The art was buried in an fpk file. Took a while to unpack and move everything over to the correct mod directories, but everything's back to normal graphic-wise.
Thanks again for your help!