As far as I know, nope. Unless you have the source code of CPW and making such functions to it.
I remember I made some changes on CPW code by the past to adapt it for Forsaken World. That's all.
The best way I would see is to add an extra function to make a special patch that will be only used to remove some files from the client (example: cpw.jar -del). And then making a normal patch that will updates the client files...