Technically, only the parts that were replaced or affected by the replacement of those parts will the warranty be voided, no matter who installs them. If a certified shop has them installed then the replaced parts should be coverd by their warranty, or if you get the dealer to do the work, they usually offer some short term warranty on workmanship/parts.
But, what really happens is the dealer (or any repair shop that accepts warranties) takes a lifted Jeep and says you abused it. Sometimes the warranty company (factory or otherwise) will call the shots as to whether the service is warrantied and you might start arguing with the wrong people. Just be ready to fight your battles (respectfully and intelligently - belligerence gets you no where) if need be.
-Marisha