No reflash, removing the battery, etc will not work. There is a flag that gets triggered in the PCM that is only there from the factory and can ONLY be set at the factory or the dealer.
The dealer CAN detect this if they're looking for it but the main question is whether or not the dealership will try to if there is an issue with the car that they suspect an ECU issue was to blame.
The reality is that yes they CAN determine that the ECU was flashed and this has been verified by another member on this or another forum who has worked with the ECU and ford.
What gives me a little peace on the matter though is that I'm not aware of anyone being denied warranty work on the engine due to a tune.
The guys who have blown their motors due to piston 8 failing all were running aftermarket tunes and all of them (as far as I know) got their engines replaced by ford with no trouble.
I honestly don't think that there is any risk of the dealer canning your warranty (remember they would have to actually PROVE that the tune was responsible for it to be valid) but this myth that flashing it back or resetting the battery and fooling the man needs to go away now because it's false.
Tunes are always a risk but I have seen no evidence to indicate that dealerships are blaming them on problems.
Edit: Here
http://www.allfordmustangs.com/forums/2554488-post42.html