Fuel Cap Dilemna

I recently purchased a used 2005 Mustang GT, and had a question about the fuel cap.

While sitting at a drive-thru looking to get some food a few days ago, my dashboard computer came up with the message to check my fuel cap. I got out and did so, and the locking gas cap on there looked good. The seal is fine and everything, but the message won't go away. I stopped at the store and filled my tank up, hoping that might fix the problem, but no such luck.

The other day, my uncle came over with his 08 GT, and we stuck his fuel cap on there...and I still got the same message.

Now here's my dilemna...when I bought the car, it came with a C&L "Street" Air Induction system, which leads us to believe that the car was also tuned by the previous owner.

We were thinking that by unplugging the battery, we could get the fuel cap code to reset...but we're also worried that this might reset the tune, and screw up my car. Any helpful advice?
 
Am having the same problem with my 09 bullitt after you reconected the battery did it take a few minutes for the car to re-learn its usual brain such as windows and things?