Original factory warranties or extended service contracts generally can not be voided in their entirety for modifications done to your motorycle. If they can prove that a modification you had done caused the failure to a component, then the coverage of that particular component would be denied but only under those conditions.
Example..you install a full exhaust system and modify your airbox, etc. Your charging system fails or your starter motor dies. Those systems are unrelated and your warranty coverage of those components can't be denied.
Several service departments I've encountered (all brands...Triumph, Honda, Kawasaki, etc) don't realize this and their standard response is "warranty denied" out of ignorance. They don't even understand how to represent the problem to the manufacturer.
If you get no satisfaction through your dealer, take it to the next level and contact the manufacturer.