Had to have Tranny re-built.

[F150 Man 4Eva]

Hello all...well things were going just great with my truck, and the custom tunes on my Gryphon, untill weekend before last. My truck was not wanting to shift into 4th (originally), then 3rd and 4th, and then it went out completely. I returned my truck to stock, removed the Gryphon, and had it towed in to the dealer. It took right at a week, but I have my truck back now. They say that the clutch went out. Seems to drive fine now. But I noticed that all my info. on the dash was reset, as if my battery was disconnected. Should I be concerned that the dealer may have reflashed the PCM? I have not attempted to reinstall the Gryphon yet, but I would like to asap. Just wondering if there are any precautions I should take, or anything I need to be aware of. Thanks, Travis