I found out the hard way not to try tune a 2011 5.0 with a Ford Pro Cal tune on it. When I read the tune out I noticed some tables didn't look stock but this was my first one using HPT and not SCT so I second guessed myself and kept going through the tune. As soon as I got to the MAF Airlfow vs Period table I knew something wasnt right for sure. It looked all jacked up and had numbers in it that were not even possible for a car to run on. I tried to enter in stock values in it and the car would not even run. I called the the customer again to verify it was stock and then they remembered it had the handheld on it. Three hours later they show up with the handheld and I return the car back to stock and then have to relicense it again . After all that I was able to tune it with no problems and made 36hp/27tq over the ford handheld.
The handheld did something that hpt cant see because no matter what you would do with the read out file from the handheld the car would run right. As soon as I read out the real stock file and made the same changes to it the car ran fine.