Intune says truck has tune but programmer is unlocked

[Xil38885]

Ok quick back story. Got the tuner a year ago put the 87 tune in it worked great. Lifted truck added 35s. Tuner would not communicate with truck anymore. Sent it back twice they said everything was fine well still didn't work. Just moved on said to hell with it lived with speedo difference. Fast forward to now just put 488 gears in it now it's running 10mph off on speedo shift points are a mess and have speed sensor issues
Got the tuner to communicate finialy after removing a few fuses. Now the problem aparently the tuner was unlocked when I sent it in but the truck is still tuned it won't let me adjust anything or re tune. What do I do besides spend $100 to reflash the thing at the dealership?

[mikel]

let it read out the files and post then here from the tunes folder on the intune drive.