You can:
a) Buy a different tool that doesn't add 3 to the flash counter each time and/or freezes the flash counter
b) Write a usermode modification that sets it to 0 on every boot.
You're probably never going to do b) if you are not able to find the flash counter in the eeprom yourself, so that leaves you with buying a tool that modifies the CBOOT so that the flash counter does not increment.
Thanks for your suggestion. Can you tell which device is good for me in this situation? I'm not professional tuner as I wrote above. I just want to write my car's ECU TCU (temic dl501 g2) over obd without hitting to any limiter.