It doesn't alter the flash counter because the software is never removed by the switch it is just turned back down to normal levels so if the dealer drove the car it feels normal and can't be picked up by normal diognostic machines. Techie may be able to comment further on this point.
Non of the remaps are completely safe or untracable
P-torque - No switch, could be flashed back to standard by p-torque but the flash counter would alter
Revo + APR - Software stays on ECU, power can be returned to standard for service etc - could be flashed back to standard by the installer but the flash counter would alter
Bluefin - Can be switched/flashed back to stock map at any time but the flash counter would alter
Custom Code - Cant comment
Hope this helps.