Yes, you can change the main folder name of them all, except geometry and textures and materials.

In P4, we use to get around the folder limit by changing pose files (pp2) to Camera files (cm2) and store them in the camera folders. I still have a bunch of stuff in my old runtime that has them there. One day I'm going to have to change them back and place them in thier proper place. Some day. LOL.