This is an excerpt from ZT warranty page on their website:
"Limited Lifetime Warranty
Zero Tolerance products are guaranteed for the lifetime of the original owner to be free of defects when received from the factory. Any product we find to be defective in its original material, construction, or workmanship will be repaired or replaced with the same item or one of equal value at no charge. (Of course, normal wear, abuse such as prying with the knife, or neglect are excluded from this non-transferable warranty.) "
Most if not all manufacturers are pretty standard with their position on warranty and modifications - they usually do not cover anything related to the modification. No different than a car or motorcycle - other than the dealer offered mods the aftermarket stuff usually voids the warranty.
Thomas regularly posts on BF and hopefully he will weigh in on this.
IMHO, I usually do not let the warranty on a knife stop me from doing something that will add to my enjoyment or functionality of the knife. Worst case for me - I have to buy a full replacement or have to buy the part that I ruined.