No nothing should happen to your engine. And they can't void your warranty unless that specific part caused the problem that your bringing it in for warranty work. So say you have the intake and you bring it in because your hub bearings are gone, they cannot void your warranty. And they shouldn't give you any trouble just for an intake.
Sometimes it just depends on the dealership. If your MAF goes bad and you have an intake installed, I can see them calling you on that one; but if you throw a rod or burn a valve, they technically have to prove that the modification caused the failure.