There are endless reasons one would need to disconnect the battery... I had to just to change my steering wheel; they can't void it off that alone..... CAN THEY?I may be reading that flow chart incorrectly, but it looks like flashing back or disconnecting the battery (aka trying to cover it up) bypasses the whole "determine if mod is culprit step and jumps straight to "cancel warranty"... It seems like your best bet is just leaving everything as is, hoping that you never overreved or screwed up your A/F ratios, and force Ford to prove that it was something that you did.
I talked to the service manager at my dealership, and he was very lawyer-esque in covering his azz, but the certified Ford Racing Tech with whom I spoke that same day said that the monkey is on Ford's back to prove that the mod caused the problem. He specifically cited the A/F ratios and any evidence of overreving the engine.
SO, what I plan on doing is just making sure that my tune doesn't raise the rev limiter and doing whatever datalogging I need to do in order to make sure everything is running like a champ. For me, the main thing is just improving the throttle response and shift points in my AT transmission. I'm not trying to milk a whole helluva lot more HP or torque out of the engine.