You are actually talking about a software update. A "flash" is a computer term that means to re-write everything at once. Basically it re-programs your trucks computer every time it is done. That way no stray data can cause issues down the...uh...road.
Your dealer should do this for free under the warranty period for sure.
Magnaflow 14" Custom Install • Bilstein 5100s Front Only Set at 2.8" • Vararam Air Grabber • Cravenspeed Stubby Antenna • Dee Zee Tailgate Assist • Billet Technology "The Punisher" Shift Knob • Debadged doors and tailgate • The Punisher Grille and Tailgate Badges • Exterior Chrome Delete • 20" XD Series 795 Hoss • LT305/55R20 Nitto Trail Grappler M/T • Cabin Air Filter • BAKFlip Roll-X Tonneau Cover