The secondary air system pumps fresh air into the exhaust stream to allow for a fuller combustion of exhaust gases. When fitting a full exhaust system and having it dyno tuned. This system needs to be removed. The valve cover has ports on it which need to be blocked with plates. The air box also gets rubber caps put on to block the holes. The reason for this is so the tuner can more accurately tune the bike without the added air being pumped in by the secondary air system messing with the A/F ratio. Some of the newer tuning flashes are able to get around more things than a basic piggy back fuel controller can and removal is not necessary.