It shouldn't if properly installed. A fuse from the battery in the amp power line is a must to prevent a fire hazard, something that the juggarroo installers always ignore. In my personal experience, I claimed warranty on the stock HU and got it replaced for free, even though sound system was installed in my 17 model city. Also sound systems, if properly installed, are really easy to remove without a trace of their installation in case you fear warranty claim denial. But in cases of fire, even if not caused by the sound system, atlas might use it as an excuse to deny warranty, you never know.