I wouldn't think that it would do anything but improve the tone. Spalted wood has no tap tone to speak of....relatively speaking. You won't hear that lovely ringing tone that you experience with a mahogany or rosewood, when you tap it with your knuckles. This type of wood is in the early stages of decay, so every piece of spalted wood will have very dense areas and softer areas, to varying degrees. With some spalts, the wood can be picked apart with your thumbnail. CPES will strengthen the wood fibers and it can be assumed, improve the tone by providing a denser material. The softer wood fibers will act as a shock absorber by not transmitting the kinetic (mechanical) energy from the strings efficiently. So by strengthening these fibers, you increase the efficiency of the string vibrations...not to mention increase sustain. I believe a spalted maple guitar build may be in my future!
GREG