SHELBY GT 350 Member
Joined: Oct 2010
Location: Desert Southwest
I don't recall seeing anything cast in stone, but the general consensus has been to load the stock tune prior to a dealer visit and to rack up at least 50 miles on it (if the car is able to do that when the day comes, assuming the engine has not been cooked somehow), as that should pack up the logs fairly well.
Another major concern (and a more legitimate one IMO) would be to remove the aftermarket tune to avoid any possible corruption, should the dealer attempt to flash over it with an update, thinking the factory tune is in the computer. You could find yourself stuck for hours or days while the dealer attempts to de-bug your computer and restart your car.
Of course, you could leave the aftermarket tune on it, tell the dealer that it's there and that you are not making any warranty claims because your engine is running just fine, and ask them to be careful to not flash any updates to it.