2012White5.0

Ok so I found out today that my car has a chip tuner that i havent know about for a year. Its been on there since I bought the car but didnt know that the switch was there till till I found it hiding in the carpet when I went to glue some of it back that had been loose. I accidentally turned it off and the car started running like crap. Since the car is stock I was wondering would it do any damage to remove it and do I just follow the install instructions that I got off American Muscle and just do it backwards.